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Description:

CEPH/UTAH PEDIGREE 1463
INTERNATIONAL HAPMAP PROJECT - CEPH (PLATE I) [UTAH RESIDENTS WITH ANCESTRY FROM NORTHERN AND WESTERN EUROPE]
CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
INTERNATIONAL HAPMAP PROJECT - CEPH [UTAH RESIDENTS WITH ANCESTRY FROM NORTHERN AND WESTERN EUROPE]
NA CUSTOM SERVICE PLATE 01

Affected:

No Data

Gender

No Data

Age:

  • Overview
  • Characterizations
  • Phenotypic Data
  • Publications
  • External Links
  • Culture Protocols

Overview

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Repository No Data
Subcollection CEPH
Repository Linkage Families
Pharmacogenetics
PIGI Consented Sample
License Required No Data
Sample Source No Data
Subject Type No Data
Family Type No Data
Ethnicity No Data
Family Member No Data
Genetic Data No Data

Characterizations

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IDENTIFICATION OF SPECIES OF ORIGIN Species of Origin Confirmed by Nucleoside Phosphorylase, Glucose-6-Phosphate Dehydrogenase, and Lactate Dehydrogenase Isoenzyme Electrophoresis
 
IDENTIFICATION OF SPECIES OF ORIGIN Species of Origin Confirmed by Nucleoside Phosphorylase, Glucose-6-Phosphate Dehydrogenase, and Lactate Dehydrogenase Isoenzyme Electrophoresis
 

Phenotypic Data

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No data is available

Publications

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Gao S, Wang Q, Gao Y, Feng X, Pang K, Li H, Zheng F, Lu J, Li B, Liu J, Yang M, Li K, Ismayiljan H, Yang H, Yan J, Guo X, Yin Y, Development and validation of a multiplex panel with 232 microhaplotypes and software for forensic kinship analysis Forensic science international Genetics76:103212 2024
PubMed ID: 39798275
 
Halligan NLN, Hanks SC, Matsuo K, Martins T, Zöllner S, Quasney MW, Scott LJ, Dahmer MK, Variants in the ß-globin locus are associated with pneumonia in African American children HGG advances6:100374 2024
PubMed ID: 39444160
 
Liao Y, Yan J, Beri NR, Giulino-Roth L, Cesarman E, Gewurz BE, Germinal center cytokine driven epigenetic control of Epstein-Barr virus latency gene expression PLoS pathogens20:e1011939 2024
PubMed ID: 38683861
 
Lima BA, Pais AC, Dupont J, Dias P, Custódio N, Sousa AB, Carmo-Fonseca M, Carvalho C, Genetic modulation of RNA splicing rescues BRCA2 function in mutant cells Life science alliance8:e1011939 2024
PubMed ID: 39741007
 
Meloche M, Pilon MO, Provost S, Leclair G, Oussaïd E, St-Jean I, Jutras M, Gaulin MJ, Lemieux Perreault LP, Valois D, Mongrain I, Busseuil D, Rouleau JL, Tardif JC, Dubé MP, de Denus S, A Genome-Wide Association Study of Oxypurinol Concentrations in Patients Treated with Allopurinol Journal of personalized medicine14:e1011939 2024
PubMed ID: 38929870
 
Middlezong W, Stinnett V, Phan M, Phan B, Morsberger L, Klausner M, Ghabrial J, DeMetrick N, Zhu J, James T, Pallavajjala A, Gocke CD, Baer MR, Zou YS, Rapid Detection of Biomolecules14:e1011939 2024
PubMed ID: 39766302
 
Quail MA, Corton C, Uphill J, Keane J, Gu Y, Identifying the best PCR enzyme for library amplification in NGS Microbial genomics10:e1011939 2024
PubMed ID: 38578268
 
Wilson TE, Ahmed S, Winningham A, Glover TW, Replication stress induces POLQ-mediated structural variant formation throughout common fragile sites after entry into mitosis Nature communications15:9582 2024
PubMed ID: 39505880
 
Xu B, Gao X, Li X, Li F, Zhang Z, Crosslinking intensity modulates the reliability and sensitivity of chromatin conformation detection at different structural levels Communications biology7:1216 2024
PubMed ID: 39349577
 
You H, Havey L, Li Z, Asara J, Guo R, Epstein-Barr-Virus-Driven Cardiolipin Synthesis Sustains Metabolic Remodeling During B-cell Lymphomagenesis Research square7:1216 2024
PubMed ID: 38659762
 
Zubiaur P, Rodríguez-Antona C, Boone EC, Daly AK, Tsermpini EE, Khasawneh LQ, Sangkuhl K, Duconge J, Botton MR, Savieo J, Nofziger C, Whirl-Carrillo M, Klein TE, Gaedigk A, PharmVar GeneFocus: CYP4F2 Clinical pharmacology and therapeutics116:963-975 2024
PubMed ID: 39135485
 
Adjemout M, Gallardo F, Torres M, Thiam A, Mbengue B, Dieye A, Marquet S, Rihet P, From Genome-wide Association Studies to Functional Variants: ARL14 Cis-regulatory Variants Are Associated With Severe Malaria The Journal of infectious diseases230:e743-e752 2023
PubMed ID: 38531688
 
Bai X, Chen Z, Chen K, Wu Z, Wang R, Liu J, Chang L, Wen L, Tang F, Simultaneous de novo calling and phasing of genetic variants at chromosome-scale using NanoStrand-seq Cell discovery10:74 2023
PubMed ID: 38977679
 
Gilpatrick T, Wang JZ, Weiss D, Norris AL, Eshleman J, Timp W, IVT generation of guideRNAs for Cas9-enrichment Nanopore Sequencing bioRxiv : the preprint server for biology10:74 2023
PubMed ID: 36798399
 
Gimeno-Valiente F, Martín-Arana J, Tébar-Martínez R, Gambardella V, Martínez-Ciarpaglini C, García-Micó B, Martínez-Castedo B, Palomar B, García-Bartolomé M, Seguí V, Huerta M, Moro-Valdezate D, Pla-Martí V, Pérez-Santiago L, Roselló S, Roda D, Cervantes A, Tarazona N, Sequencing paired tumor DNA and white blood cells improves circulating tumor DNA tracking and detects pathogenic germline variants in localized colon cancer ESMO open8:102051 2023
PubMed ID: 37951129
 
Gutierrez-Camino A, Caron M, Richer C, Fuchs C, Illarregi U, Poncelet L, St-Onge P, Bataille AR, Tremblay-Dauphinais P, Lopez-Lopez E, Camos M, Ramirez-Orellana M, Astigarraga I, Lécuyer É, Bourque G, Martin-Guerrero I, Sinnett D, CircRNAome of Childhood Acute Lymphoblastic Leukemia: Deciphering Subtype-Specific Expression Profiles and Involvement in International journal of molecular sciences25:102051 2023
PubMed ID: 38338754
 
Hansen T, Fong S, Capra JA, Hodges E, Human gene regulatory evolution is driven by the divergence of regulatory element function in both bioRxiv : the preprint server for biology25:102051 2023
PubMed ID: 36824965
 
Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey AL, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X, SJPedPanel: A pan-cancer gene panel for childhood malignancies medRxiv : the preprint server for health sciences25:102051 2023
PubMed ID: 38076942
 
Kotlov N, Shaposhnikov K, Tazearslan C, Chasse M, Baisangurov A, Podsvirova S, Fernandez D, Abdou M, Kaneunyenye L, Morgan K, Cheremushkin I, Zemskiy P, Chelushkin M, Sorokina M, Belova E, Khorkova S, Lozinsky Y, Nuzhdina K, Vasileva E, Kravchenko D, Suryamohan K, Nomie K, Curran J, Fowler N, Bagaev A, Procrustes is a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data Communications biology7:392 2023
PubMed ID: 38555407
 
Kvapilova K, Misenko P, Radvanszky J, Brzon O, Budis J, Gazdarica J, Pos O, Korabecna M, Kasny M, Szemes T, Kvapil P, Paces J, Kozmik Z, Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses BMC genomics25:187 2023
PubMed ID: 38365587
 
Liu MH, Costa B, Choi U, Bandler RC, Lassen E, Gronska-Peski M, Schwing A, Murphy ZR, Rosenkjær D, Picciotto S, Bianchi V, Stengs L, Edwards M, Loh CA, Truong TK, Brand RE, Pastinen T, Wagner JR, Skytte AB, Tabori U, Shoag JE, Evrony GD, Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing bioRxiv : the preprint server for biology25:187 2023
PubMed ID: 36824744
 
Longo GMC, Sayols S, Kotini AG, Heinen S, Möckel MM, Beli P, Roukos V, Linking CRISPR-Cas9 double-strand break profiles to gene editing precision with BreakTag Nature biotechnology25:187 2023
PubMed ID: 38740992
 
Merav M, Bitensky EM, Heilbrun EE, Hacohen T, Kirshenbaum A, Golan-Berman H, Cohen Y, Adar S, Gene architecture is a determinant of the transcriptional response to bulky DNA damages Life science alliance7:187 2023
PubMed ID: 38167611
 
Pedroza Matute S, Turvey K, Iyavoo S, Advancing human genotyping: The Infinium HTS iSelect Custom microarray panel (Rita) development study Forensic science international Genetics71:103049 2023
PubMed ID: 38653142
 
Scherthan H, Geiger B, Ridinger D, Müller J, Riccobono D, Bestvater F, Port M, Hausmann M, Nano-Architecture of Persistent Focal DNA Damage Regions in the Minipig Epidermis Weeks after Acute ?-Irradiation Biomolecules13:103049 2023
PubMed ID: 37892200
 
Sun J, Su M, Ma J, Xu M, Ma C, Li W, Liu R, He Q, Su Z, Cross-platform comparisons for targeted bisulfite sequencing of MGISEQ-2000 and NovaSeq6000 Clinical epigenetics15:130 2023
PubMed ID: 37582783
 
Sun Z, Behati S, Wang P, Bhagwate A, McDonough S, Wang V, Taylor W, Cunningham J, Kisiel J, Performance comparisons of methylation and structural variants from low-input whole-genome methylation sequencing Epigenomics15:130 2023
PubMed ID: 36919677
 
Ueda MT, Inamo J, Miya F, Shimada M, Yamaguchi K, Kochi Y, Functional and dynamic profiling of transcript isoforms reveals essential roles of alternative splicing in interferon response Cell genomics15:100654 2023
PubMed ID: 39288763
 
Uppuluri L, Shi CH, Varapula D, Young E, Ehrlich RL, Wang Y, Piazza D, Mell JC, Yip KY, Xiao M, A long-read sequencing strategy with overlapping linkers on adjacent fragments (OLAF-Seq) for targeted resequencing and enrichment Scientific reports14:5583 2023
PubMed ID: 38448490
 
Vozza G, Bonetti E, Tini G, Favalli V, Frigè G, Bucci G, De Summa S, Zanfardino M, Zapelloni F, Mazzarella L, Benchmarking and improving the performance of variant-calling pipelines with RecallME Bioinformatics (Oxford, England)39:5583 2023
PubMed ID: 38092052
 
Wu B, Li J, Wang H, Liu J, Li J, Sun F, Feng DC, RIPK1 is aberrantly expressed in multiple B-cell cancers and implicated in the underlying pathogenesis Discover Oncology14:131 2023
PubMed ID: 37462822
 
Xia Y, Katz M, Chandramohan D, Bechor E, Podgursky B, Hoxie M, Zhang Q, Chertman W, Kang J, Blue E, Chen J, Schleede J, Slotnick NR, Du X, Boostanfar R, Urcia E, Behr B, Cohen J, Siddiqui N, The first clinical validation of whole-genome screening on standard trophectoderm biopsies of preimplantation embryos F&S reports5:63-71 2023
PubMed ID: 38524212
 
Xue JR, Mackay-Smith A, Mouri K, Garcia MF, Dong MX, Akers JF, Noble M, Li X, Zoonomia Consortium† X, Lindblad-Toh K, Karlsson EK, Noonan JP, Capellini TD, Brennand KJ, Tewhey R, Sabeti PC, Reilly SK, The functional and evolutionary impacts of human-specific deletions in conserved elements Science (New York, NY)380:eabn2253 2023
PubMed ID: 37104592
 
Zollinger DR, Rivers E, Fine A, Huang Y, Son J, Kalyan A, Gray W, Baharian G, Hammond C, Ram R, Ringman L, Hafez D, Savel D, Patel V, Dantone M, Guo C, Childress M, Xu C, Johng D, Wallden B, Pokharel P, Camara W, Hegde PS, Hughes J, Carter C, Davarpanah N, Degaonkar V, Gupta P, Mariathasan S, Powles T, Ferree S, Dennis L, Young A, Analytical validation of a novel comprehensive genomic profiling informed circulating tumor DNA monitoring assay for solid tumors PloS one19:e0302129 2023
PubMed ID: 38753705
 
Adolfsson E, Kling D, Gunnarsson C, Jonasson J, Gréen H, Gréen A, Whole exome sequencing of FFPE samples-expanding the horizon of forensic molecular autopsies International journal of legal medicine19:e0302129 2022
PubMed ID: 36346469
 
Bae JH, Liu R, Roberts E, Nguyen E, Tabrizi S, Rhoades J, Blewett T, Xiong K, Gydush G, Shea D, An Z, Patel S, Cheng J, Sridhar S, Liu MH, Lassen E, Skytte AB, Gronska-Peski M, Shoag JE, Evrony GD, Parsons HA, Mayer EL, Makrigiorgos GM, Golub TR, Adalsteinsson VA, Single duplex DNA sequencing with CODEC detects mutations with high sensitivity Nature genetics55:871-879 2022
PubMed ID: 37106072
 
Battaglia S, Dong K, Wu J, Chen Z, Najm FJ, Zhang Y, Moore MM, Hecht V, Shoresh N, Bernstein BE, Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements Nature genetics54:1504-1513 2022
PubMed ID: 36195755
 
Chai H, Tjong H, Li P, Liao W, Wang P, Wong CH, Ngan CY, Leonard WJ, Wei CL, Ruan Y, ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs Nature communications14:213 2022
PubMed ID: 36639381
 
Fazel-Najafabadi M, Rallabandi HR, Singh MK, Maiti GP, Morris J, Looger LL, Nath SK, Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p131 Genes13:213 2022
PubMed ID: 35741778
 
Feng YS, Zhang C, Chen QF, Wang Y, Kang KL, Zhao J, Ji AQ, Ye J, Wang L, Evaluation of the MHSeqTyper47 kit for forensically challenging DNA samples Forensic science international Genetics61:102763 2022
PubMed ID: 35939876
 
Forgetta V, Li R, Darmond-Zwaig C, Belisle A, Balion C, Roshandel D, Wolfson C, Lettre G, Pare G, Paterson AD, Griffith LE, Verschoor C, Lathrop M, Kirkland S, Raina P, Richards JB, Ragoussis J, Cohort profile: genomic data for 26 622 individuals from the Canadian Longitudinal Study on Aging (CLSA) BMJ open12:e059021 2022
PubMed ID: 35273064
 
Füllgrabe J, Gosal WS, Creed P, Liu S, Lumby CK, Morley DJ, Ost TWB, Vilella AJ, Yu S, Bignell H, Burns P, Charlesworth T, Fu B, Fordham H, Harding NJ, Gandelman O, Golder P, Hodson C, Li M, Lila M, Liu Y, Mason J, Mellad J, Monahan JM, Nentwich O, Palmer A, Steward M, Taipale M, Vandomme A, San-Bento RS, Singhal A, Vivian J, Wójtowicz N, Williams N, Walker NJ, Wong NCH, Yalloway GN, Holbrook JD, Balasubramanian S, Simultaneous sequencing of genetic and epigenetic bases in DNA Nature biotechnology12:e059021 2022
PubMed ID: 36747096
 
Hansen TJ, Hodges E, ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome Genome research12:e059021 2022
PubMed ID: 35858748
 
Inamo J, Suzuki A, Ueda MT, Yamaguchi K, Nishida H, Suzuki K, Kaneko Y, Takeuchi T, Hatano H, Ishigaki K, Ishihama Y, Yamamoto K, Kochi Y, Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms Nature communications15:4285 2022
PubMed ID: 38806455
 
Karimnezhad A, Perkins TJ, Empirical Bayes single nucleotide variant-calling for next-generation sequencing data Scientific reports14:1550 2022
PubMed ID: 38233494
 
Lopes M, Louzada S, Ferreira D, Veríssimo G, Eleutério D, Gama-Carvalho M, Chaves R, Human Satellite 1A analysis provides evidence of pericentromeric transcription BMC biology21:28 2022
PubMed ID: 36755311
 
Lunke S, Bouffler SE, Patel CV, Sandaradura SA, Wilson M, Pinner J, Hunter MF, Barnett CP, Wallis M, Kamien B, Tan TY, Freckmann ML, Chong B, Phelan D, Francis D, Kassahn KS, Ha T, Gao S, Arts P, Jackson MR, Scott HS, Eggers S, Rowley S, Boggs K, Rakonjac A, Brett GR, de Silva MG, Springer A, Ward M, Stallard K, Simons C, Conway T, Halman A, Van Bergen NJ, Sikora T, Semcesen LN, Stroud DA, Compton AG, Thorburn DR, Bell KM, Sadedin S, North KN, Christodoulou J, Stark Z, Integrated multi-omics for rapid rare disease diagnosis on a national scale Nature medicine29:1681-1691 2022
PubMed ID: 37291213
 
Masset H, Ding J, Dimitriadou E, Debrock S, Tšuiko O, Smits K, Peeraer K, Voet T, Zamani Esteki M, Vermeesch JR, Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing Nucleic acids research50:e63 2022
PubMed ID: 35212381
 
McClinton B, Watson CM, Crinnion LA, McKibbin M, Ali M, Inglehearn CF, Toomes C, Haplotyping Using Long-Range PCR and Nanopore Sequencing of Phase Variants; Lessons Learned From the ABCA4 Locus Laboratory investigation; a journal of technical methods and pathology50:100160 2022
PubMed ID: 37088464
 
Ng JK, Vats P, Fritz-Waters E, Sarkar S, Sams EI, Padhi EM, Payne ZL, Leonard S, West MA, Prince C, Trani L, Jansen M, Vacek G, Samadi M, Harkins TT, Pohl C, Turner TN, de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project Human mutation50:100160 2022
PubMed ID: 36054329
 
Nuwan C. Hettige, Huashan Peng, Hanrong Wu, Xin Zhang, Volodymyr Yerko, Ying Zhang, Malvin Jefri, Vincent Soubannier, Gilles Maussion, Shaima Alsuwaidi, Anjie Ni, Cecilia Rocha, Jeyashree Krishnan, Vincent McCarty, Lilit Antonyan, Andreas Schuppert, Gustavo Turecki, Edward A. Fon, Thomas M. Durcan, Carl Ernst, A protocol for full-rotation soft X-ray tomography of single cells 3519903917:475-488 2022
PubMed ID: 35199039
 
Parteka-Tojek Z, Zhu JJ, Lee B, Jodkowska K, Wang P, Aaron J, Chew TL, Banecki K, Plewczynski D, Ruan Y, Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy Scientific reports12:8582 2022
PubMed ID: 35595799
 
Ramirez D, B Chuong E, D Dowell R, Nascent transcription upon interferon-a2 stimulation on human and rhesus macaque lymphoblastoid cell lines BMC research notes16:292 2022
PubMed ID: 37885027
 
Shum EY, Lai JH, Li S, Lee HG, Soliman J, Raol VK, Lee CK, Fodor SPA, Fan HC, Next-Generation Digital Polymerase Chain Reaction: High-Dynamic-Range Single-Molecule DNA Counting via Ultrapartitioning Analytical chemistry94:17868-17876 2022
PubMed ID: 36508568
 
Sinitcyn P, Richards AL, Weatheritt RJ, Brademan DR, Marx H, Shishkova E, Meyer JG, Hebert AS, Westphall MS, Blencowe BJ, Cox J, Coon JJ, Global detection of human variants and isoforms by deep proteome sequencing Nature biotechnology94:17868-17876 2022
PubMed ID: 36959352
 
Steiert TA, Fuß J, Juzenas S, Wittig M, Hoeppner MP, Vollstedt M, Varkalaite G, ElAbd H, Brockmann C, Görg S, Gassner C, Forster M, Franke A, High-throughput method for the hybridisation-based targeted enrichment of long genomic fragments for PacBio third-generation sequencing NAR genomics and bioinformatics4:lqac051 2022
PubMed ID: 35855323
 
Tilleman L, Rubben K, Van Criekinge W, Deforce D, Van Nieuwerburgh F, Haplotyping pharmacogenes using TLA combined with Illumina or Nanopore sequencing Scientific reports12:17734 2022
PubMed ID: 36273027
 
Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M, Human Pangenome Reference Consortium M, Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh P, Eichler EE, Increased mutation and gene conversion within human segmental duplications Nature617:325-334 2022
PubMed ID: 37165237
 
Wen J, Trost B, Engchuan W, Halvorsen M, Pallotto LM, Mitina A, Ancalade N, Farrell M, Backstrom I, Guo K, Pellecchia G, Thiruvahindrapuram B, Giusti-Rodriguez P, Rosen JD, Li Y, Won H, Magnusson PKE, Gyllensten U, Bassett AS, Hultman CM, Sullivan PF, Yuen RKC, Szatkiewicz JP, Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia Molecular psychiatry28:475-482 2022
PubMed ID: 36380236
 
Wright S, Zhao X, Rosikiewicz W, Mryncza S, Hyle J, Qi W, Liu Z, Yi S, Cheng Y, Xu B, Li C, Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens Nature communications14:7464 2022
PubMed ID: 38016946
 
Xu N, Shi W, Cao X, Zhou X, Jin L, Huang HF, Chen S, Xu C, Parental mosaicism detection and preimplantation genetic testing in families with multiple transmissions of de novo mutations Journal of medical genetics14:7464 2022
PubMed ID: 36707240
 
Yan B, Wang D, Vaisvila R, Sun Z, Ettwiller L, Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment Genome research32:2079-2091 2022
PubMed ID: 36332968
 
Yao X, Zhou Z, Xie Y, Huang Z, Lu S, Liu C, Wang J, Li X, Methodology established for the detection of circulating tumor DNA by hybridization capture BioTechniques73:151-158 2022
PubMed ID: 36065956
 
Zhong JY, Niu L, Lin ZB, Bai X, Chen Y, Luo F, Hou C, Xiao CL, High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding Nature communications14:1250 2022
PubMed ID: 36878904
 
Barnes AB, Keener RM, Schott BH, Wang L, Valdivia RH, Ko DC, Human genetic diversity regulating the HGG advances3:100071 2021
PubMed ID: 35047856
 
Caballero M, Ge T, Rebelo AR, Seo S, Kim S, Brooks K, Zuccaro M, Kanagaraj R, Vershkov D, Kim D, Smogorzewska A, Smolka M, Benvenisty N, West SC, Egli D, Mace EM, Koren A, Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation Human molecular genetics3:100071 2021
PubMed ID: 35394024
 
Chiu R, Rajan-Babu IS, Birol I, Friedman JM, Linked-read sequencing for detecting short tandem repeat expansions Scientific reports12:9352 2021
PubMed ID: 35672336
 
De Witte L, Raman L, Baetens M, De Koker A, Callewaert N, Symoens S, Tilleman K, Vanden Meerschaut F, Dheedene A, Menten B, GENType: all-in-one preimplantation genetic testing by pedigree haplotyping and copy number profiling suitable for third-party reproduction Human reproduction (Oxford, England)37:1678-1691 2021
PubMed ID: 35552408
 
Dubé MP, Lemaçon A, Barhdadi A, Lemieux Perreault LP, Oussaïd E, Asselin G, Provost S, Sun M, Sandoval J, Legault MA, Mongrain I, Dubois A, Valois D, Dedelis E, Lousky J, Choi J, Goulet E, Savard C, Chicoine LM, Cossette M, Chabot-Blanchet M, Guertin MC, de Denus S, Bouabdallaoui N, Marchand R, Bassevitch Z, Nozza A, Gaudet D, L'Allier PL, Hussin J, Boivin G, Busseuil D, Tardif JC, Genetics of symptom remission in outpatients with COVID-19 Scientific reports11:10847 2021
PubMed ID: 34035401
 
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Liu Z, Naler LB, Zhu Y, Deng C, Zhang Q, Zhu B, Zhou Z, Sarma M, Murray A, Xie H, Lu C, nMOWChIP-seq: low-input genome-wide mapping of non-histone targets NAR genomics and bioinformatics4:lqac030 2021
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Wang Z, Guo R, Trudeau SJ, Wolinsky E, Ast T, Liang JH, Jiang C, Ma Y, Teng M, Mootha VK, Gewurz BE, CYB561A3 is the key lysosomal iron reductase required for Burkitt B-cell growth and survival Blood138:2216-2230 2021
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Wei X, Xiang Y, Peters DT, Marius C, Sun T, Shan R, Ou J, Lin X, Yue F, Li W, Southerland KW, Diao Y, HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization Molecular cell82:1225-1238.e6 2021
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Zhang H, Rice ME, Alvin JW, Farrera-Gaffney D, Galligan JJ, Johnson MDL, Cusanovich DA, Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei BMC genomics23:214 2021
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Zhou G, Zhou M, Zeng F, Zhang N, Sun Y, Qiao Z, Guo X, Zhou S, Yun G, Xie J, Wang X, Liu F, Fan C, Wang Y, Fang Z, Tian Z, Dai W, Sun J, Peng Z, Song L, Performance characterization of PCR-free whole genome sequencing for clinical diagnosis Medicine101:e28972 2021
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Akolkar D, Patil D, Srivastava N, Patil R, Datta V, Apurwa S, Yashwante N, Dhasarathan R, Gosavi R, John J, Khan S, Jadhav N, Mene P, Ahire D, Pawar S, Bodke H, Sahoo S, Nile A, Saindane D, Darokar H, Devhare P, Srinivasan A, Datar R, Development and validation of a multigene variant profiling assay to guide targeted and immuno therapy selection in solid tumors PloS one16:e0246048 2020
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Budde BS, Aly MA, Mohamed MR, Breß A, Altmüller J, Motameny S, Kawalia A, Thiele H, Konrad K, Becker C, Toliat MR, Nürnberg G, Said EA, Mohamed ES, Pfister M, Nürnberg P, Comprehensive molecular analysis of 61 Egyptian families with hereditary nonsyndromic hearing loss Clinical genetics16:e0246048 2020
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Cheasley D, Devereux L, Hughes S, Nickson C, Procopio P, Lee G, Li N, Pridmore V, Elder K, Bruce Mann G, Kader T, Rowley SM, Fox SB, Byrne D, Saunders H, Fujihara KM, Lim B, Gorringe KL, Campbell IG, The TP53 mutation rate differs in breast cancers that arise in women with high or low mammographic density NPJ breast cancer6:34 2020
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Cheasley D, Nigam A, Zethoven M, Hunter S, Etemadmoghadam D, Semple T, Allan P, Carey MS, Fernandez ML, Dawson A, Köbel M, Huntsman DG, Page CL, Mes-Masson AM, Provencher D, Hacker N, Gao Y, Bowtell D, de Fazio A, Gorringe KL, Campbell IG, Genomic analysis of low-grade serous ovarian carcinoma to identify key drivers and therapeutic vulnerabilities The Journal of pathology6:34 2020
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Conconi D, Redaelli S, Lissoni AA, Cilibrasi C, Perego P, Gautiero E, Sala E, Paderno M, Dalprà L, Landoni F, Lavitrano M, Roversi G, Bentivegna A, Genomic and Epigenomic Profile of Uterine Smooth Muscle Tumors of Uncertain Malignant Potential (STUMPs) Revealed Similarities and Differences with Leiomyomas and Leiomyosarcomas International journal of molecular sciences22:34 2020
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Deng C, Murphy TW, Zhang Q, Naler LB, Xu A, Lu C, Multiplexed and Ultralow-Input ChIP-seq Enabled by Tagmentation-Based Indexing and Facile Microfluidics Analytical chemistry22:34 2020
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Dong Z, Chau MHK, Zhang Y, Yang Z, Shi M, Wah YM, Kwok YK, Leung TY, Morton CC, Choy KW, Low-pass genome sequencing-based detection of absence of heterozygosity: validation in clinical cytogenetics Genetics in medicine : official journal of the American College of Medical Genetics23:1225-1233 2020
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Goodwin PJ, Dowling RJO, Ennis M, Chen BE, Parulekar WR, Shepherd LE, Burnell MJ, Vander Meer R, Molckovsky A, Gurjal A, Gelmon KA, Ligibel JA, Hershman DL, Mayer IA, Whelan TJ, Hobday TJ, Rastogi P, Rabaglio-Poretti M, Lemieux J, Thompson AM, Rea DW, Stambolic V, NPJ breast cancer7:74 2020
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Gorla A, Jew B, Zhang L, Sul JH, xGAP: A python based efficient, modular, extensible and fault tolerant genomic analysis pipeline for variant discovery Bioinformatics (Oxford, England)7:74 2020
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Granja JM, Corces MR, Pierce SE, Bagdatli ST, Choudhry H, Chang HY, Greenleaf WJ, ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis Nature genetics53:403-411 2020
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Graybuck LT, Daigle TL, Sedeño-Cortés AE, Walker M, Kalmbach B, Lenz GH, Morin E, Nguyen TN, Garren E, Bendrick JL, Kim TK, Zhou T, Mortrud M, Yao S, Siverts LA, Larsen R, Gore BB, Szelenyi ER, Trader C, Balaram P, van Velthoven CTJ, Chiang M, Mich JK, Dee N, Goldy J, Cetin AH, Smith K, Way SW, Esposito L, Yao Z, Gradinaru V, Sunkin SM, Lein E, Levi BP, Ting JT, Zeng H, Tasic B, Enhancer viruses for combinatorial cell-subclass-specific labeling Neuron109:1449-1464.e13 2020
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Koren A, Massey DJ, Bracci AN, TIGER: inferring DNA replication timing from whole-genome sequence data Bioinformatics (Oxford, England)109:1449-1464.e13 2020
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McKerrow W, Tang Z, Steranka JP, Payer LM, Boeke JD, Keefe D, Fenyö D, Burns KH, Liu C, Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells Philosophical transactions of the Royal Society of London Series B, Biological sciences375:20190335 2020
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Min YK, Lee YK, Nam SH, Kim JK, Park KS, Kim JW, Quantitative and Qualitative QC of Next-Generation Sequencing for Detecting Somatic Variants: An Example of Detecting Clonal Hematopoiesis of Indeterminate Potential Clinical chemistry375:20190335 2020
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Park K, Tran H, Eng KW, Ramazanoglu S, Marrero Rolon RM, Scognamiglio T, Borczuk A, Mosquera JM, Pan Q, Sboner A, Rubin MA, Elemento O, Rennert H, Fernandes H, Song W, Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome Archives of pathology & laboratory medicine375:20190335 2020
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Parsons HA, Rhoades J, Reed SC, Gydush G, Ram P, Exman P, Xiong K, Lo CC, Li T, Fleharty M, Kirkner GJ, Rotem D, Cohen O, Yu F, Fitarelli-Kiehl M, Leong KW, Hughes ME, Rosenberg SM, Collins LC, Miller KD, Blumenstiel B, Trippa L, Cibulskis C, Neuberg DS, DeFelice M, Freeman SS, Lennon NJ, Wagle N, Ha G, Stover DG, Choudhury AD, Getz G, Winer EP, Meyerson M, Lin NU, Krop I, Love JC, Makrigiorgos GM, Partridge AH, Mayer EL, Golub TR, Adalsteinsson V, Sensitive detection of minimal residual disease in patients treated for early-stage breast cancer Clinical cancer research : an official journal of the American Association for Cancer Research375:20190335 2020
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Payne A, Holmes N, Clarke T, Munro R, Debebe BJ, Loose M, Readfish enables targeted nanopore sequencing of gigabase-sized genomes Nature biotechnology375:20190335 2020
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Plongthongkum N, Diep D, Chen S, Lake BB, Zhang K, Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2) Nature protocols16:4992-5029 2020
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Psyrri A, Gkotzamanidou M, Papaxoinis G, Krikoni L, Economopoulou P, Kotsantis I, Anastasiou M, Souliotis VL, The DNA damage response network in the treatment of head and neck squamous cell carcinoma ESMO open6:100075 2020
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Ramudo-Cela L, López-Martí JM, Colmeiro-Echeberría D, De-Uña-Iglesias D, Santomé-Collazo JL, Monserrat-Iglesias L, Development and validation of a next-generation sequencing panel for clinical pharmacogenetics Farmacia hospitalaria : organo oficial de expresion cientifica de la Sociedad Espanola de Farmacia Hospitalaria44:243-253 2020
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Ren H, Xi Y, Li Z, Zhang D, Huang F, Fang X, Zhao X, Zhang X, Chen A, Chen T, Jiang Y, Novel target capture DNA library preparation method using CircLigase-mediated hook ligation New biotechnology59:44-50 2020
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Schwessinger R, Gosden M, Downes D, Brown RC, Oudelaar AM, Telenius J, Teh YW, Lunter G, Hughes JR, DeepC: predicting 3D genome folding using megabase-scale transfer learning Nature methods17:1118-1124 2020
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Trinchant NM, MacKay MJ, Chin C, Afshinnekoo E, Foox J, Meydan C, Butler D, Mozsary C, Vernice NA, Darby C, Schatz MC, Bailey SM, Melnick AM, Guzman M, Bolton K, Braunstein LZ, Garrett-Bakelman F, Levine RL, Hassane D, Mason CE, Clonal Hematopoiesis Before, During, and After Human Spaceflight Cell reports13:108458 2020
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Ullmann R, Becker BV, Rothmiller S, Schmidt A, Thiermann H, Kaatsch HL, Schrock G, Müller J, Jakobi J, Obermair R, Port M, Scherthan H, Genomic Adaption and Mutational Patterns in a HaCaT Subline Resistant to Alkylating Agents and Ionizing Radiation International journal of molecular sciences22:108458 2020
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Wong KHY, Ma W, Wei CY, Yeh EC, Lin WJ, Wang EHF, Su JP, Hsieh FJ, Kao HJ, Chen HH, Chow SK, Young E, Chu C, Poon A, Yang CF, Lin DS, Hu YF, Wu JY, Lee NC, Hwu WL, Boffelli D, Martin D, Xiao M, Kwok PY, Towards a reference genome that captures global genetic diversity Nature communications11:5482 2020
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Xu M, Guo L, Gu S, Wang O, Zhang R, Peters BA, Fan G, Liu X, Xu X, Deng L, Zhang Y, TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads GigaScience9:5482 2020
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Azad AK, Huang CK, Jin H, Zou H, Yanakakis L, Du J, Fiddler M, Naeem R, Goldstein Y, Enhanced Carrier Screening for Spinal Muscular Atrophy: Detection of Silent (SMN1: 2 + 0) Carriers Utilizing a Novel TaqMan Genotyping Method Laboratory medicine68:573-580 2019
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Bullerwell CE, Robichaud PP, Deprez PML, Joy AP, Wajnberg G, D'Souza D, Chacko S, Fournier S, Crapoulet N, Barnett DA, Lewis SM, Ouellette RJ, EBF1 drives hallmark B cell gene expression by enabling the interaction of PAX5 with the MLL H3K4 methyltransferase complex Scientific reports11:1537 2019
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Chaubey A, Shenoy S, Mathur A, Ma Z, Valencia CA, Reddy Nallamilli BR, Szekeres E, Stansberry L, Liu R, Hegde MR, Low-Pass Genome Sequencing: Validation and Diagnostic Utility from 409 Clinical Cases of Low-Pass Genome Sequencing for the Detection of Copy Number Variants to Replace Constitutional Microarray The Journal of molecular diagnostics : JMD22:823-840 2019
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Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M, Ultra-low input single tube linked-read library method enables short-read second-generation sequencing systems to generate highly accurate and economical long-range sequencing information routinely Genome research9:9345 2019
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Factor DC, Barbeau AM, Allan KC, Hu LR, Madhavan M, Hoang AT, Hazel KEA, Hall PA, Nisraiyya S, Najm FJ, Miller TE, Nevin ZS, Karl RT, Lima BR, Song Y, Sibert AG, Dhillon GK, Volsko C, Bartels CF, Adams DJ, Dutta R, Gallagher MD, Phu W, Kozlenkov A, Dracheva S, Scacheri PC, Tesar PJ, Corradin O, Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS Cell181:382-395.e21 2019
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Fujiki R, Ikeda M, Ohara O, Short DNA Probes Developed for Sample Tracking and Quality Assurance in Gene Panel Testing The Journal of molecular diagnostics : JMD181:382-395.e21 2019
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Gaedigk A, Turner A, Everts RE, Scott SA, Aggarwal P, Broeckel U, McMillin GA, Melis R, Boone EC, Pratt VM, Kalman LV, Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles A GeT-RM Collaborative Project The Journal of molecular diagnostics : JMD181:382-395.e21 2019
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Guo R, Zhang Y, Teng M, Jiang C, Schineller M, Zhao B, Doench JG, O'Reilly RJ, Cesarman E, Giulino-Roth L, Gewurz BE, DNA methylation enzymes and PRC1 restrict B-cell Epstein-Barr virus oncoprotein expression Nature microbiology181:382-395.e21 2019
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Heft IE, Mostovoy Y, Levy-Sakin M, Ma W, Stevens AJ, Pastor S, McCaffrey J, Boffelli D, Martin DI, Xiao M, Kennedy MA, Kwok PY, Sikela JM, The Driver of Extreme Human-Specific Olduvai Repeat Expansion Remains Highly Active in the Human Genome Genetics181:382-395.e21 2019
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Hu J, Li W, Adebali O, Yang Y, Oztas O, Selby CP, Sancar A, Genome-wide mapping of nucleotide excision repair with XR-seq Nature Protocols14:248-282 2019
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Izevbaye I, Liang LY, Mather C, El-Hallani S, Maglantay R, Saini L, Clinical Validation of a Myeloid Next-Generations Sequencing Panel for Single Nucleotide Variants, Indels, and Fusion Genes The Journal of molecular diagnostics : JMD14:248-282 2019
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Jenkins MM, Almli LM, Pangilinan F, Chong JX, Blue EE, Shapira SK, White J, McGoldrick D, Smith JD, Mullikin JC, Bean CJ, Nembhard WN, Lou XY, Shaw GM, Romitti PA, Keppler-Noreuil K, Yazdy MM, Kay DM, Carter TC, Olshan AF, Moore KJ, Nascone-Yoder N, Finnell RH, Lupo PJ, Feldkamp ML, NISC Comparative Sequencing Program ML, University of Washington Center for Mendelian Genomics ML, Nickerson DA, Bamshad MJ, Brody LC, Reefhuis J, National Birth Defects Prevention Study J, Exome sequencing of family trios from the National Birth Defects Prevention Study: Tapping into a rich resource of genetic and environmental data Birth defects research14:248-282 2019
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Kader T, Elder K, Zethoven M, Semple T, Hill P, Goode DL, Thio N, Cheasley D, Rowley SM, Byrne DJ, Pang JM, Miligy IM, Green AR, Rakha EA, Fox SB, Mann GB, Campbell IG, Gorringe KL, The genetic architecture of breast papillary lesions as a predictor of progression to carcinoma NPJ breast cancer6:9 2019
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Kathuria K, Ratan A, SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures PLoS computational biology16:e1007737 2019
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Koboldt DC, Best practices for variant calling in clinical sequencing Genome medicine12:91 2019
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Lazzarotto CR, Malinin NL, Li Y, Zhang R, Yang Y, Lee G, Cowley E, He Y, Lan X, Jividen K, Katta V, Kolmakova NG, Petersen CT, Qi Q, Strelcov E, Maragh S, Krenciute G, Ma J, Cheng Y, Tsai SQ, CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity Nature biotechnology12:91 2019
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Lee J, Heo S, Bang D, Applying a Linear Amplification Strategy to Recombinase Polymerase Amplification for Uniform DNA Library Amplification ACS omega4:19953-19958 2019
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Leung ML, Watson DJ, Vaccaro CN, Mafra F, Wenocur A, Wang T, Hakonarson H, Santani A, Evaluating sequence data quality from the Swift Accel-Amplicon CFTR Panel Scientific data7:8 2019
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Liu C, Zhang Y, Li X, Jia Y, Li F, Li J, Zhang Z, Evidence of constraint in the 3D genome for trans-splicing in human cells Science China Life sciences7:8 2019
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Lu L, Liu X, Huang WK, Giusti-Rodríguez P, Cui J, Zhang S, Xu W, Wen Z, Ma S, Rosen JD, Xu Z, Bartels CF, Kawaguchi R, Hu M, Scacheri PC, Rong Z, Li Y, Sullivan PF, Song H, Ming GL, Li Y, Jin F, Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases Molecular cell7:8 2019
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Massey DJ, Kim D, Brooks KE, Smolka MB, Koren A, Next-Generation Sequencing Enables Spatiotemporal Resolution of Human Centromere Replication Timing Genes10:8 2019
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McCabe MJ, Gauthier MA, Chan CL, Thompson TJ, De Sousa SMC, Puttick C, Grady JP, Gayevskiy V, Tao J, Ying K, Cipponi A, Deng N, Swarbrick A, Thomas ML, Lord RV, Johns AL, Kohonen-Corish M, O'Toole SA, Clark J, Mueller SA, Gupta R, McCormack AI, Dinger ME, Cowley MJ, kConFab MJ, Development and validation of a targeted gene sequencing panel for application to disparate cancers Scientific reports9:17052 2019
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McClain L, Segreti AM, Nau S, Shaw P, Finegold DN, Pan LA, Peters DG, Chromosome 15q133 microduplications are associated with treatment refractory major depressive disorder Genes, brain, and behavior9:e12628 2019
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Miyao A, Kiyomiya JS, Iida K, Doi K, Yasue H, Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data BMC bioinformatics20:362 2019
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Orchard P, Kyono Y, Hensley J, Kitzman JO, Parker SCJ, Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv Cell systems10:298-306.e4 2019
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Osorio D, Yu X, Zhong Y, Li G, Yu P, Serpedin E, Huang JZ, Cai JJ, Single-Cell Expression Variability Implies Cell Function Cells9:298-306.e4 2019
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Quinodoz SA, Bhat P, Chovanec P, Jachowicz JW, Ollikainen N, Detmar E, Soehalim E, Guttman M, SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding Nature protocols17:36-75 2019
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Razavi P, Li BT, Brown DN, Jung B, Hubbell E, Shen R, Abida W, Juluru K, De Bruijn I, Hou C, Venn O, Lim R, Anand A, Maddala T, Gnerre S, Vijaya Satya R, Liu Q, Shen L, Eattock N, Yue J, Blocker AW, Lee M, Sehnert A, Xu H, Hall MP, Santiago-Zayas A, Novotny WF, Isbell JM, Rusch VW, Plitas G, Heerdt AS, Ladanyi M, Hyman DM, Jones DR, Morrow M, Riely GJ, Scher HI, Rudin CM, Robson ME, Diaz LA, Solit DB, Aravanis AM, Reis-Filho JS, High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants Nature medicine25:1928-1937 2019
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Rosenthal SH, Sun W, Zhang K, Liu Y, Nguyen Q, Gerasimova A, Nery C, Cheng L, Castonguay C, Hiller E, Li J, Elzinga C, Wolfson D, Smolgovsky A, Chen R, Buller-Burckle A, Catanese J, Grupe A, Lacbawan F, Owen R, Development and Validation of a 34-Gene Inherited Cancer Predisposition Panel Using Next-Generation Sequencing BioMed research international2020:3289023 2019
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Sangkuhl K, Whirl-Carrillo M, Whaley RM, Woon M, Lavertu A, Altman RB, Carter L, Verma A, Ritchie MD, Klein TE, Pharmacogenomics Clinical Annotation Tool (PharmCAT) Clinical pharmacology and therapeutics2020:3289023 2019
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Sarma M, Lee J, Ma S, Li S, Lu C, A diffusion-based microfluidic device for single-cell RNA-seq Lab on a chip2020:3289023 2019
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Toss MS, Abidi A, Lesche D, Joseph C, Mahale S, Saunders H, Kader T, Miligy IM, Green AR, Gorringe KL, Rakha EA, The prognostic significance of immune microenvironment in breast ductal carcinoma in situ British journal of cancer5:41 2019
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Trzaskoma P, Ruszczycki B, Lee B, Pels KK, Krawczyk K, Bokota G, Szczepankiewicz AA, Aaron J, Walczak A, Sliwinska MA, Magalska A, Kadlof M, Wolny A, Parteka Z, Arabasz S, Kiss-Arabasz M, Plewczynski D, Ruan Y, Wilczynski GM, Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization Nature communications11:2120 2019
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Twesigomwe D, Wright GEB, Drögemöller BI, da Rocha J, Lombard Z, Hazelhurst S, A systematic comparison of pharmacogene star allele calling bioinformatics algorithms: a focus on NPJ genomic medicine5:30 2019
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Wang LW, Wang Z, Ersing I, Nobre L, Guo R, Jiang S, Trudeau S, Zhao B, Weekes MP, Gewurz BE, Epstein-Barr virus subverts mevalonate and fatty acid pathways to promote infected B-cell proliferation and survival PLoS pathogens15:e1008030 2019
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Yamaguchi I, Watanabe T, Ohara O, Hasegawa Y, PCR-free whole exome sequencing: Cost-effective and efficient in detecting rare mutations PloS one14:e0222562 2019
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Andrew M. Gross PhD, Subramanian S. Ajay PhD, Vani Rajan MS, Carolyn Brown CGC, Krista Bluske PhD, Nicole J. Burns MS, Aditi Chawla PhD, Alison J. Coffey PhD, Alka Malhotra PhD, Alicia Scocchia MS CGC, Erin Thorpe MS CGC, Natasa Dzidic MS, Karine Hovanes PhD FACMG, Trilochan Sahoo MD FACMG, Egor Dolzhenko PhD, Bryan Lajoie PhD, Amirah Khouzam MS CGC, Shimul Chowdhury PhD FACMG, John Belmont MD PhD, Eric Roller PhD, Sergii Ivakhno PhD, Stephen Tanner PhD, Julia McEachern PA MHS, Tina Hambuch PhD FACMG, Michael Eberle PhD, R. Tanner Hagelstrom PhD FACMG, David R. Bentley PhD, Denise L. Perry MS CGC & Ryan J. Taft PhD, Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease Genetics in Medicine20:71 2018
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Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE, Characterizing the Major Structural Variant Alleles of the Human Genome Cell176:663-675.e19 2018
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Balajee AS1, Sanders JT2, Golloshi R2, Shuryak I3, McCord RP2, Dainiak N, Investigation of Spatial Organization of Chromosome Territories in Chromosome Exchange Aberrations After Ionizing Radiation Exposure Health Physics115:77-89 2018
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Ben Aim L, Pigny P, Castro-Vega LJ, Buffet A, Amar L, Bertherat J, Drui D, Guilhem I, Baudin E, Lussey-Lepoutre C, Corsini C, Chabrier G, Briet C, Faivre L, Cardot-Bauters C, Favier J, Gimenez-Roqueplo AP, Burnichon N, Targeted next-generation sequencing detects rare genetic events in pheochromocytoma and paraganglioma Journal of medical genetics115:77-89 2018
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Blombery P, Jones K, Doig K, Ryland G, McBean M, Thompson E, Yannakou CK, Westerman D, Sensitive NPM1 Mutation Quantitation in Acute Myeloid Leukemia Using Ultradeep Next-Generation Sequencing in the Diagnostic Laboratory Archives of pathology & laboratory medicine115:77-89 2018
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Bowden R, Davies RW, Heger A, Pagnamenta AT, de Cesare M, Oikkonen LE, Parkes D, Freeman C, Dhalla F, Patel SY, Popitsch N, Ip CLC, Roberts HE, Salatino S, Lockstone H, Lunter G, Taylor JC, Buck D, Simpson MA, Donnelly P, Sequencing of human genomes with nanopore technology Nature communications10:1869 2018
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Cheasley D, Wakefield MJ, Ryland GL, Allan PE, Alsop K, Amarasinghe KC, Ananda S, Anglesio MS, Au-Yeung G, Böhm M, Bowtell DDL, Brand A, Chenevix-Trench G, Christie M, Chiew YE, Churchman M, DeFazio A, Demeo R, Dudley R, Fairweather N, Fedele CG, Fereday S, Fox SB, Gilks CB, Gourley C, Hacker NF, Hadley AM, Hendley J, Ho GY, Hughes S, Hunstman DG, Hunter SM, Jobling TW, Kalli KR, Kaufmann SH, Kennedy CJ, Köbel M, Le Page C, Li J, Lupat R, McNally OM, McAlpine JN, Mes-Masson AM, Mileshkin L, Provencher DM, Pyman J, Rahimi K, Rowley SM, Salazar C, Samimi G, Saunders H, Semple T, Sharma R, Sharpe AJ, Stephens AN, Thio N, Torres MC, Traficante N, Xing Z, Zethoven M, Antill YC, Scott CL, Campbell IG, Gorringe KL, The molecular origin and taxonomy of mucinous ovarian carcinoma Nature communications10:3935 2018
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Giner-Delgado C, Villatoro S, Lerga-Jaso J, Gayà-Vidal M, Oliva M, Castellano D, Pantano L, Bitarello BD, Izquierdo D, Noguera I, Olalde I, Delprat A, Blancher A, Lalueza-Fox C, Esko T, O'Reilly PF, Andrés AM, Ferretti L, Puig M, Cáceres M, Evolutionary and functional impact of common polymorphic inversions in the human genome Nature communications10:4222 2018
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Harwood JC, Kent NA, Allen ND, Harwood AJ, Nucleosome dynamics of human iPSC during neural differentiation EMBO reports20:4222 2018
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Johnston AD, Simões-Pires CA, Thompson TV, Suzuki M, Greally JM, Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding Nature communications10:3472 2018
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Kajitani R, Yoshimura D, Okuno M, Minakuchi Y, Kagoshima H, Fujiyama A, Kubokawa K, Kohara Y, Toyoda A, Itoh T, Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions Nature communications10:1702 2018
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Kim D, Paggi JM, Park C, Bennett C, Salzberg SL, Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Nature biotechnology37:907-915 2018
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Lazzarotto CR1, Nguyen NT2,3, Tang X1, Malagon-Lopez J2,4,5, Guo JA2, Aryee MJ2,4,5, Joung JK2,4, Tsai SQ6., Defining CRISPR-Cas9 genome-wide nuclease activities with CIRCLE-seq Nat Protoc13:2615-2642 2018
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Lee J, Lim H, Jang H, Hwang B, Lee JH, Cho J, Lee JH, Bang D, CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system Nucleic acids research13:2615-2642 2018
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Lincoln SE, Truty R, Lin CF, Zook JM, Paul J, Ramey VH, Salit M, Rehm HL, Nussbaum RL, Lebo MS, A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing-Detected Variants with an Orthogonal Method in Clinical Genetic Testing The Journal of molecular diagnostics : JMD13:2615-2642 2018
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Ma ZS, Li L, Ye C, Peng M, Zhang YP, Hybrid assembly of ultra-long Nanopore reads augmented with 10x-Genomics contigs: Demonstrated with a human genome Genomics13:2615-2642 2018
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Maggiolini FAM, Cantsilieris S, D'Addabbo P, Manganelli M, Coe BP, Dumont BL, Sanders AD, Pang AWC, Vollger MR, Palumbo O, Palumbo P, Accadia M, Carella M, Eichler EE, Antonacci F, Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus PLoS genetics15:e1008075 2018
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Michael J. Keogh, Wei Wei, Juvid Aryaman, Lauren Walker, Jelle van den Ameele, Jon Coxhead, Ian Wilson, Matthew Bashton, Jon Beck, John West, Richard Chen, Christian Haudenschild, Gabor Bartha, Shujun Luo, Chris M. Morris, Nick S. Jones, Johannes Attems & Patrick F. Chinnery, High prevalence of focal and multi-focal somatic genetic variants in the human brain Nature Communications9:4257 2018
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Mitsuhashi S, Frith MC, Mizuguchi T, Miyatake S, Toyota T, Adachi H, Oma Y, Kino Y, Mitsuhashi H, Matsumoto N, Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads Genome biology20:58 2018
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Mumbach MR, Granja JM, Flynn RA, Roake CM, Satpathy AT, Rubin AJ, Qi Y, Jiang Z, Shams S, Louie BH, Guo JK, Gennert DG, Corces MR, Khavari PA, Atianand MK, Artandi SE, Fitzgerald KA, Greenleaf WJ, Chang HY, HiChIRP reveals RNA-associated chromosome conformation Nature methods16:489-492 2018
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Peng Q, Xu C, Kim D, Lewis M, DiCarlo J, Wang Y, Targeted Single Primer Enrichment Sequencing with Single End Duplex-UMI Scientific reports9:4810 2018
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Pliner HA1, Packer JS1, McFaline-Figueroa JL1, Cusanovich DA1, Daza RM1, Aghamirzaie D1, Srivatsan S1, Qiu X2, Jackson D1, Minkina A1, Adey AC3, Steemers FJ4, Shendure J5, Trapnell C6., Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data Molecular Cell9:4810 2018
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Quinodoz SA1, Ollikainen N1, Tabak B2, Palla A1, Schmidt JM1, Detmar E1, Lai MM1, Shishkin AA1, Bhat P3, Takei Y1, Trinh V1, Aznauryan E1, Russell P4, Cheng C5, Jovanovic M6, Chow A1, Cai L1, McDonel P2, Garber M2, Guttman M, Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus Cell174:744-757 2018
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Stephen Bruinsma, Joshua Burgess, Daniel Schlingman, Agata Czyz, Natalie Morrell, Catherine Ballenger, Heather Meinholz, Lee Brady, Anupama Khanna, Lindsay Freeberg, Rosamond G Jackson, Pascale Mathonet, Susan C Verity, Andrew F Slatter, Rooz Golshani, Haiying Grunenwald, Gary P Schroth and Niall A Gormley, Bead-linked transposomes enable a normalization-free workflow for NGS library preparation BMC Genomics19:722 2018
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Velasco G, Grillo G, Touleimat N, Ferry L, Ivkovic I, Ribierre F, Deleuze JF, Chantalat S, Picard C, Francastel C, Comparative methylome analysis of ICF patients identifies heterochromatin loci that require ZBTB24, CDCA7 and HELLS for their methylated state Human molecular genetics21:491-502 2018
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Wang LW, Shen H, Nobre L, Ersing I, Paulo JA, Trudeau S, Wang Z, Smith NA, Ma Y, Reinstadler B, Nomburg J, Sommermann T, Cahir-McFarland E, Gygi SP, Mootha VK, Weekes MP, Gewurz BE, Epstein-Barr-Virus-Induced One-Carbon Metabolism Drives B Cell Transformation Cell metabolism21:491-502 2018
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Yeeok Kang, Seong-Hyeuk Nam, Kyung Sun Park, Yoonjung Kim, Jong-Won Kim, Eunjung Lee, Jung Min Ko, Kyung-A Lee and Inho ParkEmail, DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data BMC Bioinformatics19:491-502 2018
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Shigemizu D, Miya F, Akiyama S, Okuda S, Boroevich KA, Fujimoto A, Nakagawa H, Ozaki K, Niida S, Kanemura Y, Okamoto N, Saitoh S, Kato M, Yamasaki M, Matsunaga T, Mutai H, Kosaki K, Tsunoda T, IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis Scientific reports8:5608 2017
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Soukupova J, Zemankova P, Lhotova K, Janatova M, Borecka M, Stolarova L, Lhota F, Foretova L, Machackova E, Stranecky V, Tavandzis S, Kleiblova P, Vocka M, Hartmannova H, Hodanova K, Kmoch S, Kleibl Z, Validation of CZECANCA (CZEch CAncer paNel for Clinical Application) for targeted NGS-based analysis of hereditary cancer syndromes PloS one13:e0195761 2017
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Trost B, Walker S, Wang Z, Thiruvahindrapuram B, MacDonald JR, Sung WWL, Pereira SL, Whitney J, Chan AJS, Pellecchia G, Reuter MS, Lok S, Yuen RKC, Marshall CR, Merico D, Scherer SW, A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data American journal of human genetics102:142-155 2017
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dbSNP dbSNP ID: 623
Gene Cards CYP2C19
CYP2C19
Gene Ontology GO:0004497 monooxygenase activity
GO:0004497 monooxygenase activity
GO:0005783 endoplasmic reticulum
GO:0005783 endoplasmic reticulum
GO:0005792 microsome
GO:0005792 microsome
GO:0006118 electron transport
GO:0006118 electron transport
GO:0016020 membrane
GO:0016020 membrane
GO:0018676 (S)-limonene 7-monooxygenase activity
GO:0018676 (S)-limonene 7-monooxygenase activity
GO:0019825 oxygen binding
GO:0019825 oxygen binding
GEO GEO Accession No: GSM1002650
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GEO Accession No: GSM1333986
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GEO Accession No: GSM1333988
GEO Accession No: GSM1333989
GEO Accession No: GSM1333990
GEO Accession No: GSM1333991
GEO Accession No: GSM1333992
GEO Accession No: GSM1333993
GEO Accession No: GSM1333994
GEO Accession No: GSM1333995
GEO Accession No: GSM1333996
GEO Accession No: GSM1333997
GEO Accession No: GSM1333998
GEO Accession No: GSM1333999
GEO Accession No: GSM1334000
GEO Accession No: GSM1334001
GEO Accession No: GSM1334002
GEO Accession No: GSM1334003
GEO Accession No: GSM1334004
GEO Accession No: GSM1334005
GEO Accession No: GSM1334006
GEO Accession No: GSM1334007
GEO Accession No: GSM1334008
GEO Accession No: GSM1334009
GEO Accession No: GSM1334010
GEO Accession No: GSM1334011
GEO Accession No: GSM1334012
GEO Accession No: GSM1368907
GEO Accession No: GSM1368911
GEO Accession No: GSM1395233
GEO Accession No: GSM1395234
GEO Accession No: GSM188847
GEO Accession No: GSM189029
GEO Accession No: GSM230072
GEO Accession No: GSM230073
GEO Accession No: GSM245656
GEO Accession No: GSM252744
GEO Accession No: GSM252745
GEO Accession No: GSM252763
GEO Accession No: GSM252764
GEO Accession No: GSM253632
GEO Accession No: GSM285268
GEO Accession No: GSM285269
GEO Accession No: GSM285270
GEO Accession No: GSM285307
GEO Accession No: GSM285308
GEO Accession No: GSM320156
GEO Accession No: GSM320157
GEO Accession No: GSM320158
GEO Accession No: GSM320159
GEO Accession No: GSM320160
GEO Accession No: GSM320161
GEO Accession No: GSM320162
GEO Accession No: GSM320163
GEO Accession No: GSM320164
GEO Accession No: GSM363727
GEO Accession No: GSM363728
GEO Accession No: GSM363729
GEO Accession No: GSM363730
GEO Accession No: GSM363731
GEO Accession No: GSM363732
GEO Accession No: GSM363733
GEO Accession No: GSM363734
GEO Accession No: GSM363735
GEO Accession No: GSM363743
GEO Accession No: GSM363744
GEO Accession No: GSM363745
GEO Accession No: GSM363746
GEO Accession No: GSM421093
GEO Accession No: GSM484895
GEO Accession No: GSM484896
GEO Accession No: GSM485683
GEO Accession No: GSM486316
GEO Accession No: GSM486317
GEO Accession No: GSM486318
GEO Accession No: GSM486319
GEO Accession No: GSM486320
GEO Accession No: GSM486321
GEO Accession No: GSM486494
GEO Accession No: GSM486495
GEO Accession No: GSM486496
GEO Accession No: GSM486497
GEO Accession No: GSM486498
GEO Accession No: GSM486499
GEO Accession No: GSM486500
GEO Accession No: GSM486501
GEO Accession No: GSM486502
GEO Accession No: GSM487429
GEO Accession No: GSM487430
GEO Accession No: GSM487431
GEO Accession No: GSM503372
GEO Accession No: GSM503373
GEO Accession No: GSM503374
GEO Accession No: GSM503375
GEO Accession No: GSM503376
GEO Accession No: GSM503377
GEO Accession No: GSM608157
GEO Accession No: GSM608158
GEO Accession No: GSM646522
GEO Accession No: GSM651106
GEO Accession No: GSM651107
GEO Accession No: GSM660003
GEO Accession No: GSM660210
GEO Accession No: GSM660416
GEO Accession No: GSM672834
GEO Accession No: GSM683774
GEO Accession No: GSM683841
GEO Accession No: GSM683906
GEO Accession No: GSM683927
GEO Accession No: GSM714692
GEO Accession No: GSM714695
GEO Accession No: GSM714697
GEO Accession No: GSM733642
GEO Accession No: GSM733664
GEO Accession No: GSM733677
GEO Accession No: GSM733679
GEO Accession No: GSM733708
GEO Accession No: GSM733736
GEO Accession No: GSM733742
GEO Accession No: GSM733752
GEO Accession No: GSM733758
GEO Accession No: GSM733767
GEO Accession No: GSM733769
GEO Accession No: GSM733771
GEO Accession No: GSM733772
GEO Accession No: GSM736496
GEO Accession No: GSM736620
GEO Accession No: GSM748510
GEO Accession No: GSM748511
GEO Accession No: GSM748512
GEO Accession No: GSM748526
GEO Accession No: GSM748527
GEO Accession No: GSM748528
GEO Accession No: GSM748529
GEO Accession No: GSM748530
GEO Accession No: GSM749669
GEO Accession No: GSM749704
GEO Accession No: GSM749706
GEO Accession No: GSM758559
GEO Accession No: GSM758560
GEO Accession No: GSM758572
GEO Accession No: GSM759538
GEO Accession No: GSM765386
GEO Accession No: GSM767852
GEO Accession No: GSM767853
GEO Accession No: GSM803338
GEO Accession No: GSM803341
GEO Accession No: GSM803342
GEO Accession No: GSM803346
GEO Accession No: GSM803347
GEO Accession No: GSM803349
GEO Accession No: GSM803350
GEO Accession No: GSM803351
GEO Accession No: GSM803355
GEO Accession No: GSM803356
GEO Accession No: GSM803362
GEO Accession No: GSM803363
GEO Accession No: GSM803386
GEO Accession No: GSM803387
GEO Accession No: GSM803388
GEO Accession No: GSM803389
GEO Accession No: GSM803390
GEO Accession No: GSM803391
GEO Accession No: GSM803392
GEO Accession No: GSM803406
GEO Accession No: GSM803411
GEO Accession No: GSM803413
GEO Accession No: GSM803416
GEO Accession No: GSM803420
GEO Accession No: GSM803434
GEO Accession No: GSM803436
GEO Accession No: GSM803477
GEO Accession No: GSM803485
GEO Accession No: GSM803496
GEO Accession No: GSM803508
GEO Accession No: GSM803509
GEO Accession No: GSM803510
GEO Accession No: GSM803511
GEO Accession No: GSM803531
GEO Accession No: GSM803532
GEO Accession No: GSM803534
GEO Accession No: GSM803537
GEO Accession No: GSM803538
GEO Accession No: GSM816665
GEO Accession No: GSM822270
GEO Accession No: GSM822290
GEO Accession No: GSM822292
GEO Accession No: GSM822312
GEO Accession No: GSM828355
GEO Accession No: GSM828367
GEO Accession No: GSM828369
GEO Accession No: GSM830534
GEO Accession No: GSM830535
GEO Accession No: GSM849329
GEO Accession No: GSM849341
GEO Accession No: GSM849348
GEO Accession No: GSM849349
GEO Accession No: GSM849352
GEO Accession No: GSM849368
GEO Accession No: GSM864360
GEO Accession No: GSM922975
GEO Accession No: GSM922976
GEO Accession No: GSM923451
GEO Accession No: GSM944519
GEO Accession No: GSM944520
GEO Accession No: GSM944524
GEO Accession No: GSM944525
GEO Accession No: GSM945188
GEO Accession No: GSM945196
GEO Accession No: GSM945212
GEO Accession No: GSM945259
GEO Accession No: GSM958728
GEO Accession No: GSM958730
GEO Accession No: GSM958742
GEO Accession No: GSM970289
GEO Accession No: GSM970499
GEO Accession No: GSM999285
GEO Accession No: GSM999376
GEO Accession No: GSM999410
NCBI Gene Gene ID:1557
Gene ID:1557
NCBI GTR 124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
OMIM 124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19
124020 CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 19; CYP2C19

Culture Protocols

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Split Ratio 1:6
Temperature 37 C
Percent CO2 5%
Percent O2 AMBIENT
Medium Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent
Serum 15% fetal bovine serum Not Inactivated
Substrate None specified
Subcultivation Method dilution - add fresh medium
Supplement -
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