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An introduction to the Y-chromosomal data from Phase 3 of the 1000 Genomes Project

An introduction to the Y-chromosomal data from Phase 3 of the 1000 Genomes Project. Yali Xue on behalf of The 1000 Genomes Y chromosome group. Crossing over in PAR1 - 2.6Mb. Crossing over in PAR2 - 0.32Mb. Workable part of Y chromosome. Unique region ~10.4 Mb SNPs, Indels & MNPs callable.

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An introduction to the Y-chromosomal data from Phase 3 of the 1000 Genomes Project

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  1. An introduction to the Y-chromosomal data from Phase 3 of the 1000 Genomes Project Yali Xue on behalf of The 1000 Genomes Y chromosome group

  2. Crossing over in PAR1 - 2.6Mb Crossing over in PAR2 - 0.32Mb Workable part of Y chromosome Unique region ~10.4 Mb SNPs, Indels & MNPs callable STRs SVs callable Male-specific region ~ 55Mb Y

  3. Release dataset * Not included in the official release 1000Y group

  4. Sample and haplogroup distribution FIN CEU GBR TSI IBS CHB JPT ASW CDX MXL CHS ACB KHV PUR CLM BEB PEL GIH GWD MSL LWK YRI ESN STU PJL ITU

  5. SNP-based phylogeny Illumina low coverage data, biallelic SNPs only A-T B-T DE C F-T R Including high coverage Complete Genomics data David Poznik, Carlos Bustamante Yali Xue, Yuan Chen

  6. Contrasting recent expansions Europe I1 R1a R1b Sub-saharan Africa E1b David Poznik, Carlos Bustamante

  7. Contrasting recent expansions South Asia L R2 H East Asia O3 David Poznik, Carlos Bustamante

  8. Chromosomal anomalies HG02372: 47,XXY (100%) Klinefelter syndrome, ~1 in 1000 live male births, often undiagnosed HG00246 46,XY (38%) 45,XO (62%) Bob Handsaker, David Poznik Ruby Banerjee, Fengtang Yang

  9. SVs Bob Handsaker, Seva Kashin

  10. SVs 2.5 Mb deletion removing AMELY and other genes in 4 males (3 hg J2; 1 hg R1a) Bob Handsaker, Seva Kashin Andrea Massaia, aCGH group

  11. Functional Variants Two stop-gained SNPs, both singletons, were found Qasim Ayub, Yuan Chen

  12. Conclusions • Diverse high-quality variant set • Robust phylogeny • New insights into male history • Data available: • Link:

  13. Acknowledgements: 1000Y group Goncalo Abecasis Adam Auton David Poznik Vincenza Colonna Qasim Ayub Suganthi Bala Carlos Bustamante Yuan Chen Laura Clarke Lachlan Coin Richard Durbin Yaniv Erlich Fuli Yu Erik Garrison Mark Gerstein Ivenise Carrero Gonzalez Bob Handsaker Ryan Hernandez Zamin Iqbal Jeffrey Rosenfeld Luke Jostins Goo Jun Seva Kashin Jan Korbel Gerstein Lab (Weng) Charles Lee Brooks Lisa Andrea Massaia Shane McCarthy Gil McVean David Mittelman Apurva Narechania Juan Rodriguez-Flores Haojing Shao Chris Tyler-Smith Peter Underhill Yekaterina Vaydylevich Alistair Ward Thomas Frederick Willems Jinchuan Xing Yali Xue Kai Ye Fan Zhang Ruibang Luo Additional members of several of these labs Poster 1992M 3:00PM-4:00PM on Mon

  14. Haplogroups

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