Dr Shane A. McCarthy | Senior Scientific Manager

McCarthy, Shane A.

shane.mccarthy@sanger.ac.uk
Vertebrate ResequencingDurbin Group

Publications

  • A reference panel of 64,976 haplotypes for genotype imputation.

    McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR et al.

    Nature genetics 2016;48;10;1279-83

    PUBMED: 27548312; PMC: 5388176; DOI: 10.1038/ng.3643

  • A global reference for human genetic variation.

    1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP et al.

    Nature 2015;526;7571;68-74

    PUBMED: 26432245; PMC: 4750478; DOI: 10.1038/nature15393

  • Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.

    Huang J, Howie B, McCarthy S, Memari Y, Walter K et al.

    Nature communications 2015;6;8111

    PUBMED: 26368830; PMC: 4579394; DOI: 10.1038/ncomms9111

  • An integrated map of genetic variation from 1,092 human genomes.

    1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA et al.

    Nature 2012;491;7422;56-65

    PUBMED: 23128226; PMC: 3498066; DOI: 10.1038/nature11632

  • Insights into hominid evolution from the gorilla genome sequence.

    Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I et al.

    Nature 2012;483;7388;169-75

    PUBMED: 22398555; PMC: 3303130; DOI: 10.1038/nature10842

  • BCFtools/csq: haplotype-aware variant consequences.

    Danecek P and McCarthy SA

    Bioinformatics (Oxford, England) 2017;33;13;2037-2039

    PUBMED: 28205675; PMC: 5870570; DOI: 10.1093/bioinformatics/btx100

  • Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome.

    Shi W, Massaia A, Louzada S, Handsaker J, Chow W et al.

    Genome biology 2019;20;1;207

    PUBMED: 31610793; PMC: 6790999; DOI: 10.1186/s13059-019-1816-y

  • Crumble: reference free lossy compression of sequence quality values.

    Bonfield JK, McCarthy SA and Durbin R

    Bioinformatics (Oxford, England) 2019;35;2;337-339

    PUBMED: 29992288; PMC: 6330002; DOI: 10.1093/bioinformatics/bty608

  • BCFtools/csq: haplotype-aware variant consequences.

    Danecek P and McCarthy SA

    Bioinformatics (Oxford, England) 2017;33;13;2037-2039

    PUBMED: 28205675; PMC: 5870570; DOI: 10.1093/bioinformatics/btx100

  • Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity.

    Hendricks AE, Bochukova EG, Marenne G, Keogh JM, Atanassova N et al.

    Scientific reports 2017;7;1;4394

    PUBMED: 28663568; PMC: 5491520; DOI: 10.1038/s41598-017-03054-8

  • Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations.

    Xue Y, Mezzavilla M, Haber M, McCarthy S, Chen Y et al.

    Nature communications 2017;8;15927

    PUBMED: 28643794; PMC: 5490002; DOI: 10.1038/ncomms15927

  • Common genetic variation drives molecular heterogeneity in human iPSCs.

    Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K et al.

    Nature 2017;546;7658;370-375

    PUBMED: 28489815; PMC: 5524171; DOI: 10.1038/nature22403

  • Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom.

    Chheda H, Palta P, Pirinen M, McCarthy S, Walter K et al.

    European journal of human genetics : EJHG 2017;25;4;477-484

    PUBMED: 28145424; PMC: 5346294; DOI: 10.1038/ejhg.2016.205

  • Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7.

    Luo Y, de Lange KM, Jostins L, Moutsianas L, Randall J et al.

    Nature genetics 2017;49;2;186-192

    PUBMED: 28067910; PMC: 5289625; DOI: 10.1038/ng.3761

  • Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.

    Dolle DD, Liu Z, Cotten M, Simpson JT, Iqbal Z et al.

    Genome research 2017;27;2;300-309

    PUBMED: 27986821; PMC: 5287235; DOI: 10.1101/gr.211748.116

  • Whole-exome sequencing of 228 patients with sporadic Parkinson's disease.

    Sandor C, Honti F, Haerty W, Szewczyk-Krolikowski K, Tomlinson P et al.

    Scientific reports 2017;7;41188

    PUBMED: 28117402; DOI: 10.1038/srep41188

  • Reference-based phasing using the Haplotype Reference Consortium panel.

    Loh PR, Danecek P, Palamara PF, Fuchsberger C, A Reshef Y et al.

    Nature genetics 2016;48;11;1443-1448

    PUBMED: 27694958; PMC: 5096458; DOI: 10.1038/ng.3679

  • A reference panel of 64,976 haplotypes for genotype imputation.

    McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR et al.

    Nature genetics 2016;48;10;1279-83

    PUBMED: 27548312; PMC: 5388176; DOI: 10.1038/ng.3643

  • Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.

    Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A et al.

    Nature genetics 2016;48;6;593-9

    PUBMED: 27111036; PMC: 4884158; DOI: 10.1038/ng.3559

  • Health and population effects of rare gene knockouts in adult humans with related parents.

    Narasimhan VM, Hunt KA, Mason D, Baker CL, Karczewski KJ et al.

    Science (New York, N.Y.) 2016;352;6284;474-7

    PUBMED: 26940866; PMC: 4985238; DOI: 10.1126/science.aac8624

  • Deep Roots for Aboriginal Australian Y Chromosomes.

    Bergström A, Nagle N, Chen Y, McCarthy S, Pollard MO et al.

    Current biology : CB 2016;26;6;809-13

    PUBMED: 26923783; PMC: 4819516; DOI: 10.1016/j.cub.2016.01.028

  • A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.

    Danecek P, McCarthy SA, HipSci Consortium and Durbin R

    PloS one 2016;11;5;e0155014

    PUBMED: 27176002; PMC: 4866717; DOI: 10.1371/journal.pone.0155014

  • A global reference for human genetic variation.

    1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP et al.

    Nature 2015;526;7571;68-74

    PUBMED: 26432245; PMC: 4750478; DOI: 10.1038/nature15393

  • An integrated map of structural variation in 2,504 human genomes.

    Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A et al.

    Nature 2015;526;7571;75-81

    PUBMED: 26432246; PMC: 4617611; DOI: 10.1038/nature15394

  • Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.

    Zheng HF, Forgetta V, Hsu YH, Estrada K, Rosello-Diez A et al.

    Nature 2015;526;7571;112-7

    PUBMED: 26367794; PMC: 4755714; DOI: 10.1038/nature14878

  • Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.

    Huang J, Howie B, McCarthy S, Memari Y, Walter K et al.

    Nature communications 2015;6;8111

    PUBMED: 26368830; PMC: 4579394; DOI: 10.1038/ncomms9111

  • Whole-genome sequence-based analysis of thyroid function.

    Taylor PN, Porcu E, Chew S, Campbell PJ, Traglia M et al.

    Nature communications 2015;6;5681

    PUBMED: 25743335; PMC: 4366514; DOI: 10.1038/ncomms6681

  • A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.

    Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G et al.

    Nature communications 2014;5;4871

    PUBMED: 25225788; PMC: 4167609; DOI: 10.1038/ncomms5871

  • A calibrated human Y-chromosomal phylogeny based on resequencing.

    Wei W, Ayub Q, Chen Y, McCarthy S, Hou Y et al.

    Genome research 2013;23;2;388-95

    PUBMED: 23038768; PMC: 3561879; DOI: 10.1101/gr.143198.112

  • Jdp2 downregulates Trp53 transcription to promote leukaemogenesis in the context of Trp53 heterozygosity.

    van der Weyden L, Rust AG, McIntyre RE, Robles-Espinoza CD, del Castillo Velasco-Herrera M et al.

    Oncogene 2013;32;3;397-402

    PUBMED: 22370638; PMC: 3550594; DOI: 10.1038/onc.2012.56

  • An integrated map of genetic variation from 1,092 human genomes.

    1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA et al.

    Nature 2012;491;7422;56-65

    PUBMED: 23128226; PMC: 3498066; DOI: 10.1038/nature11632

  • Insights into hominid evolution from the gorilla genome sequence.

    Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I et al.

    Nature 2012;483;7388;169-75

    PUBMED: 22398555; PMC: 3303130; DOI: 10.1038/nature10842

  • Path to fracture in granular flows: dynamics of contact networks.

    Herrera M, McCarthy S, Slotterback S, Cephas E, Losert W and Girvan M

    Physical review. E, Statistical, nonlinear, and soft matter physics 2011;83;6 Pt 1;061303

    PUBMED: 21797354; DOI: 10.1103/PhysRevE.83.061303

McCarthy, Shane A.
Shane's Links
Shane's Timeline
2014

Team leader, Vertebrate Resequencing

2013

Principal Bioinformatician, Vertebrate Resequencing

2012

UK10K Project Production co-chair

2010

Joined Vertebrate Resequencing team at Sanger as Senior Bioinformatician

2009

MPhil in Computational Biology, University of Cambridge

2008

Research Associate, Institute for Research in Electronics and Applied Physics, University of Maryland

2006

Research Associate, Center for String and Particle Theory, University of Maryland

2001

Began PhD in Physics, University of Western Australia

2000

Completed BSc (Hons) in Physics and Pure Mathematics, University of Western Autralia