Dr Qasim Ayub | Staff Scientist

This person is a member of Sanger Institute Alumni.

Ayub, Qasim

I have been working with the Human Evolution Team at the Wellcome Trust Sanger Institute, Hinxton, United Kingdom, since 2008. My research focuses on the analyses of DNA variation in human and primate genomes in order to understand how humans adapted to local diets, environments and pathogens as they established themselves in different parts of the world. I developed a method that can be used to universally test for positive selection and adaptation signals in different gene sets and populations using whole-genome sequencing data. I continue to maintain my interest in human Y chromosomal variation and South Asian population genomics in health and disease.

I graduated from the Khyber Medical College, Peshawar, Pakistan and obtained my Ph.D. from the University of North Texas, Denton, Texas in 1992 on a Thomas Jefferson Fellowship. Back in Pakistan I joined the Biomedical and Genetic Engineering Laboratories that became the focal point for the Human Genome Diversity Project’s South Asian sample collection. Over the last decade I have analyzed DNA variation in ethnic and linguistic groups from Pakistan, with a particular emphasis on Y chromosomal variation, in order to understand their genetic origins and relatedness with world populations. In 2006 I was awarded the President of Pakistan’s Medal of Excellence for contributions to science.

Publications

  • Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas.

    Hackinger S, Kraaijenbrink T, Xue Y, Mezzavilla M, Asan et al.

    Human genetics 2016;135;4;393-402

  • 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

  • The Kalash genetic isolate: ancient divergence, drift, and selection.

    Ayub Q, Mezzavilla M, Pagani L, Haber M, Mohyuddin A et al.

    American journal of human genetics 2015;96;5;775-83

  • Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding.

    Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q et al.

    Science (New York, N.Y.) 2015;348;6231;242-245

  • Revisiting the thrifty gene hypothesis via 65 loci associated with susceptibility to type 2 diabetes.

    Ayub Q, Moutsianas L, Chen Y, Panoutsopoulou K, Colonna V et al.

    American journal of human genetics 2014;94;2;176-85

  • FOXP2 targets show evidence of positive selection in European populations.

    Ayub Q, Yngvadottir B, Chen Y, Xue Y, Hu M et al.

    American journal of human genetics 2013;92;5;696-706

  • 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

  • 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

  • A systematic survey of loss-of-function variants in human protein-coding genes.

    MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J et al.

    Science (New York, N.Y.) 2012;335;6070;823-8

  • Genetic variation in South Asia: assessing the influences of geography, language and ethnicity for understanding history and disease risk.

    Ayub Q and Tyler-Smith C

    Briefings in functional genomics & proteomics 2009;8;5;395-404

  • Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas.

    Hackinger S, Kraaijenbrink T, Xue Y, Mezzavilla M, Asan et al.

    Human genetics 2016;135;4;393-402

  • 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

  • Monoamine Oxidase A gene polymorphisms and self reported aggressive behaviour in a Pakistani ethnic group.

    Shah SS, Mohyuddin A, Colonna V, Mehdi SQ and Ayub Q

    JPMA. The Journal of the Pakistan Medical Association 2015;65;8;818-24

  • Copy number variation in the human Y chromosome in the UK population.

    Wei W, Fitzgerald TW, Fitzgerald T, Ayub Q, Massaia A et al.

    Human genetics 2015;134;7;789-800

  • Erratum to: Copy number variation in the human Y chromosome in the UK population.

    Wei W, Fitzgerald TW, Ayub Q, Massaia A, Smith BH et al.

    Human genetics 2015;134;7;801

  • Structural variation on the human Y chromosome from population-scale resequencing.

    Espinosa JR, Ayub Q, Chen Y, Xue Y and Tyler-Smith C

    Croatian medical journal 2015;56;3;194-207

  • The Kalash genetic isolate: ancient divergence, drift, and selection.

    Ayub Q, Mezzavilla M, Pagani L, Haber M, Mohyuddin A et al.

    American journal of human genetics 2015;96;5;775-83

  • Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding.

    Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q et al.

    Science (New York, N.Y.) 2015;348;6231;242-245

  • A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

    Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M et al.

    Genome research 2015;25;4;459-66

  • Identification of new SNPs in native South American populations by resequencing the Y chromosome.

    Geppert M, Ayub Q, Xue Y, Santos S, Ribeiro-dos-Santos  et al.

    Forensic science international. Genetics 2015;15;111-4

  • A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.

    Clemente FJ, Cardona A, Inchley CE, Peter BM, Jacobs G et al.

    American journal of human genetics 2014;95;5;584-589

  • A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

    Purps J, Siegert S, Willuweit S, Nagy M, Alves C et al.

    Forensic science international. Genetics 2014;12;12-23

  • Toward male individualization with rapidly mutating y-chromosomal short tandem repeats.

    Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ et al.

    Human mutation 2014;35;8;1021-32

  • Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

    Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P et al.

    Genome biology 2014;15;6;R88

  • Revisiting the thrifty gene hypothesis via 65 loci associated with susceptibility to type 2 diabetes.

    Ayub Q, Moutsianas L, Chen Y, Panoutsopoulou K, Colonna V et al.

    American journal of human genetics 2014;94;2;176-85

  • A comparison of Y-chromosomal lineage dating using either resequencing or Y-SNP plus Y-STR genotyping.

    Wei W, Ayub Q, Xue Y and Tyler-Smith C

    Forensic science international. Genetics 2013;7;6;568-72

  • Integrative annotation of variants from 1092 humans: application to cancer genomics.

    Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM et al.

    Science (New York, N.Y.) 2013;342;6154;1235587

  • FOXP2 targets show evidence of positive selection in European populations.

    Ayub Q, Yngvadottir B, Chen Y, Xue Y, Hu M et al.

    American journal of human genetics 2013;92;5;696-706

  • 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

  • A genome-wide survey of genetic variation in gorillas using reduced representation sequencing.

    Scally A, Yngvadottir B, Xue Y, Ayub Q, Durbin R and Tyler-Smith C

    PloS one 2013;8;6;e65066

  • Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.

    Xue Y, Chen Y, Ayub Q, Huang N, Ball EV et al.

    American journal of human genetics 2012;91;6;1022-32

  • 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

  • Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool.

    Pagani L, Tarekegn A, Ekong R, Plaster C, Gallego Romero I et al.

    American journal of human genetics 2012;91;1;83-96

  • Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.

    Hu M, Ayub Q, Guerra-Assunção JA, Long Q, Ning Z et al.

    Human genetics 2012;131;5;665-74

  • 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

  • High altitude adaptation in Daghestani populations from the Caucasus.

    Pagani L, Ayub Q, MacArthur DG, Xue Y, Baillie JK et al.

    Human genetics 2012;131;3;423-33

  • A systematic survey of loss-of-function variants in human protein-coding genes.

    MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J et al.

    Science (New York, N.Y.) 2012;335;6070;823-8

  • Male lineages in the Himalayan foothills: a commentary on Y-chromosome haplogroup diversity in the sub-Himalayan Terai and Duars populations of East India.

    Ayub Q

    Journal of human genetics 2011;56;12;813-4

  • The variant call format and VCFtools.

    Danecek P, Auton A, Abecasis G, Albers CA, Banks E et al.

    Bioinformatics (Oxford, England) 2011;27;15;2156-8

  • Demographic history and rare allele sharing among human populations.

    Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT et al.

    Proceedings of the National Academy of Sciences of the United States of America 2011;108;29;11983-8

  • Variation in genome-wide mutation rates within and between human families.

    Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y et al.

    Nature genetics 2011;43;7;712-4

  • Mapping copy number variation by population-scale genome sequencing.

    Mills RE, Walter K, Stewart C, Handsaker RE, Chen K et al.

    Nature 2011;470;7332;59-65

  • Diversity of human copy number variation and multicopy genes.

    Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M et al.

    Science (New York, N.Y.) 2010;330;6004;641-6

  • A map of human genome variation from population-scale sequencing.

    1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD et al.

    Nature 2010;467;7319;1061-73

  • Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a.

    Underhill PA, Myres NM, Rootsi S, Metspalu M, Zhivotovsky LA et al.

    European journal of human genetics : EJHG 2010;18;4;479-84

  • A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations.

    Shi W, Ayub Q, Vermeulen M, Shao RG, Zuniga S et al.

    Molecular biology and evolution 2010;27;2;385-93

  • Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation.

    Xue Y, Zhang X, Huang N, Daly A, Gillson CJ et al.

    Genetics 2009;183;3;1065-77

  • Genetic variation in South Asia: assessing the influences of geography, language and ethnicity for understanding history and disease risk.

    Ayub Q and Tyler-Smith C

    Briefings in functional genomics & proteomics 2009;8;5;395-404

  • A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia.

    Dhandapany PS, Sadayappan S, Xue Y, Powell GT, Rani DS et al.

    Nature genetics 2009;41;2;187-91

  • Mapping of a novel type III variant of Knobloch syndrome (KNO3) to chromosome 17q11.2.

    Khaliq S, Abid A, White DR, Johnson CA, Ismail M et al.

    American journal of medical genetics. Part A 2007;143A;23;2768-74

  • Human leukocyte antigen (HLA) class II association with rheumatic heart disease in Pakistan.

    Rehman S, Akhtar N, Ahmad W, Ayub Q, Mehdi SQ and Mohyuddin A

    The Journal of heart valve disease 2007;16;3;300-4

  • Association between the angiotensin-converting enzyme gene insertion/deletion polymorphism and essential hypertension in young Pakistani patients.

    Ismail M, Akhtar N, Nasir M, Firasat S, Ayub Q and Khaliq S

    Journal of biochemistry and molecular biology 2004;37;5;552-5

  • Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor.

    Quintana-Murci L, Chaix R, Wells RS, Behar DM, Sayar H et al.

    American journal of human genetics 2004;74;5;827-45

  • Investigation of the Greek ancestry of populations from northern Pakistan.

    Mansoor A, Mazhar K, Khaliq S, Hameed A, Rehman S et al.

    Human genetics 2004;114;5;484-90

  • Genetic instability in EBV-transformed lymphoblastoid cell lines.

    Mohyuddin A, Ayub Q, Siddiqi S, Carvalho-Silva DR, Mazhar K et al.

    Biochimica et biophysica acta 2004;1670;1;81-3

  • Reconstruction of human evolutionary tree using polymorphic autosomal microsatellites.

    Ayub Q, Mansoor A, Ismail M, Khaliq S, Mohyuddin A et al.

    American journal of physical anthropology 2003;122;3;259-68

  • The genetic legacy of the Mongols.

    Zerjal T, Xue Y, Bertorelle G, Wells RS, Bao W et al.

    American journal of human genetics 2003;72;3;717-21

  • HLA polymorphism in six ethnic groups from Pakistan.

    Mohyuddin A, Ayub Q, Khaliq S, Mansoor A, Mazhar K et al.

    Tissue antigens 2002;59;6;492-501

  • Y-chromosomal DNA variation in Pakistan.

    Qamar R, Ayub Q, Mohyuddin A, Helgason A, Mazhar K et al.

    American journal of human genetics 2002;70;5;1107-24

  • Y-chromosomal STR haplotypes in Pakistani populations.

    Mohyuddin A, Ayub Q, Qamar R, Zerjal T, Helgason A et al.

    Forensic science international 2001;118;2-3;141-6

  • Y-chromosome lineages trace diffusion of people and languages in southwestern Asia.

    Quintana-Murci L, Krausz C, Zerjal T, Sayar SH, Hammer MF et al.

    American journal of human genetics 2001;68;2;537-42

  • Identification and characterisation of novel human Y-chromosomal microsatellites from sequence database information.

    Ayub Q, Mohyuddin A, Qamar R, Mazhar K, Zerjal T et al.

    Nucleic acids research 2000;28;2;e8

  • HLA polymorphisms in ethnic groups from Pakistan.

    Mohyuddin A, Ayub Q, Qamar R, Khaliq S, Mansoor A and Mehdi SQ

    Transplantation proceedings 1999;31;8;3350-1

  • African and Levantine origins of Pakistani YAP+ Y chromosomes.

    Qamar R, Ayub Q, Khaliq S, Mansoor A, Karafet T et al.

    Human biology 1999;71;5;745-55

Ayub, Qasim