Working Group Series

The PQG will host another monthly working group series for the 2014-2015 school year. Please see the full list of dates and speakers below, as they continue to be updated.

Each year, the PQG organizes a less formal working group seminar for all local students, postdocs, and faculty. The goal is to provide the opportunity to present and participate in the discussion of works-in-progress, and to focus on the methods and analysis of high-dimensional data in genetics and genomics.


Organizer: Po-Ru Loh

Please direct any logistical questions to Shaina Andelman

 

Upcoming Working Group



Tuesday, December 2, 2014
12:30-2:00 PM
Building 2, Room 426 - Biostatistics Conference Room
a pizza lunch will be provided

Sriram Sankararaman
Postdoc
Reich Lab at Harvard Medical School

Characterizing the structure and impact of archaic admixture in humans

Large-scale studies of human genetic variation, in conjunction with advances in ancient DNA technology, have revealed a number of mixture events between highly-diverged human populations that occurred tens of thousands of years ago (archaic admixture), e.g., between the ancestors of Neandertals and modern non-Africans. While several subsequent studies have found examples of phenotypically-relevant genetic variants introduced by archaic admixture, the biological impact of archaic admixture on human populations is not systematically understood. To understand the biological impact, we need maps of archaic local ancestry i.e., a labeling of the archaic ancestry along an individual genome.

We developed a statistical method based on the framework of Conditional Random Fields (CRF) and applied it to infer Neandertal local ancestry. The CRF provides inferences that are robust and sensitive both on simulated and real data. We applied the CRF to data from the 1000 Genomes project combined with a high-coverage Neandertal genome. The resulting map of Neandertal local ancestry reveals likely positive selection of Neandertal ancestry in specific loci and sets of genes (e.g. genes involved in keratin filament formation), associations between Neandertal-derived alleles and medical phenotypes (e.g. Crohn's disease), as well as strong purifying selection against Neandertal alleles in part due to the effects of hybrid male sterility.

Finally, I will present ongoing work to study the impact of another archaic admixture between a population known as Denisovans and ancestors of modern Melanesian populations. I will discuss generalizations of the CRF to multi-way and de-novo admixtures as well as unphased data, efforts to study phenotypic associations of Neandertal variants and some open statistical questions ( how do we learn and apply discriminative models to population genetic problems?).

2014-2015 Working Groups


  • Tuesday, October 7, 2014
    12:30-2:00 PM
    Building 2, Room 426 - Biostatistics Conference Room
    Elinor Karlsson, Sabeti Lab at Harvard

  • Tuesday, October 28, 2014
    12:30-2:00 PM
    Building 2, Room 426 - Biostatistics Conference Room
    Yun Li, University North Carolina at Chapel Hill

  • Tuesday, December 2, 2014
    12:30-2:00 PM
    Building 2, Room 426 - Biostatistics Conference Room
    Sriram Sankararaman, Reich Lab at Harvard Medical School


  • Tuesday, January 20, 2015
    12:30-2:00 PM
    Building 2, Room 426 - Biostatistics Conference Room
    Manuel Rivas, Broad Institute

  • Tuesday, February 24, 2015
    12:30-2:00 PM
    Building 2, Room 426 - Biostatistics Conference Room
    Jason Flannick, Altshuler Lab at Broad Institute

  • Tuesday, March 24, 2015
    12:30-2:00 PM
    Building 2, Room 426 - Biostatistics Conference Room
    Daniel Balick, Sunyaev Lab at Brigham & Women's Hospital

  • Tuesday, April 21, 2015
    12:30-2:00 PM
    Building 2, Room 426 - Biostatistics Conference Room
    Rany Salem, Hirschhorn Lab at Boston Children's Hospital

  • Tuesday, May 12, 2015
    12:30-2:00 PM
    Building 2, Room 426 - Biostatistics Conference Room
    Jae-Hoon Sul, Sunyaev Lab at Brigham & Women's Hospital


 

Working Group Archive

 

Please feel free to contact us with any comments or questions at: sandelma@hsph.harvard.edu