News

Talk on haplotype-informed CNV analysis at ProbGen 2022

March 16, 2022
At the 2022 Probabilistic Modeling in Genomics (ProbGen) conference, Margaux Hujoel will be presenting her work on haplotype-informed CNV detection and subsequent association and fine-mapping analysis in UK Biobank: "Influences of rare copy number variation on human complex traits" (Mon Mar 28).

Po-Ru Loh receives 2022 ISCB Overton Prize

February 19, 2022
Po-Ru Loh has been awarded the International Society for Computational Biology's Overton Prize for outstanding accomplishment by an early to mid-career scientist in the field of computational biology. A big thank-you to all of the mentors, collaborators, and trainees who contributed to the work recognized by this award! Po-Ru will be accepting the award and presenting a keynote talk at the ISMB 2022 conference in July.

New preprint on phenotypes observed in carriers of recessive disease variants

December 14, 2021
We are excited to share a new preprint, "A spectrum of recessiveness among Mendelian disease variants in UK Biobank" (Barton et al.), which leverages whole-exome sequencing together with imputation in UK Biobank to identify carrier effects of rare variants known to cause recessive Mendelian diseases in homozygotes. These analyses identified 103 significant associations between quantitative traits and carrier status for 35 unique Mendelian recessive diseases, including a... Read more about New preprint on phenotypes observed in carriers of recessive disease variants

New preprint on phenotypic impacts of rare copy number variants

October 22, 2021
We are excited to share a new preprint, "Influences of rare copy number variation on human complex traits" (Hujoel et al.), which explores the phenotypic impact of rare copy number variation in the human genome, discovering many new ways in which genetic variation shapes human traits. These analyses were enabled by a new computational approach we developed that substantially increases CNV detection power in large cohorts by pooling information across individuals who... Read more about New preprint on phenotypic impacts of rare copy number variants

Protein-coding variable number tandem repeat (VNTR) paper published in Science

September 23, 2021
Ronen Mukamel and Bob Handsaker's paper on phenotypic effects of protein-coding variable-number-of-tandem repeat (VNTR) polymorphisms (Mukamel*, Handsaker* et al. 2021 Science) is now published -- congratulations, Ronen and Bob! This exciting collaboration with Steve McCarroll's lab found that some of the largest effects of common genetic variants on human phenotypes (including height, biomarkers of health, and hair morphology) arise... Read more about Protein-coding variable number tandem repeat (VNTR) paper published in Science

Three talks and a poster talk at ASHG 2021

August 23, 2021

We're very excited to share our ongoing work at ASHG this October! Alison Barton and Margaux Hujoel will present platform talks on penetrance of disease variants and CNV associations in UK Biobank, Maxwell Sherman will present a plenary talk on somatic mutations in cancer, and Ronen Mukamel will present a poster talk on dissecting Lp(a) genetics. Alison, Margaux, and Max all received semifinalist Charles J. Epstein Trainee Awards -- congratulations!

Alison Barton: "Incomplete penetrance of disease variants in the UK Biobank" (platform talk, Wed 10/20 at 11:15am)...

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New preprint on learning patterns of somatic mutation in cancer

August 4, 2021
We are excited to share a new preprint, "Learning the mutational landscape of the cancer genome" (Sherman*, Yaari*, Priebe* et al.). This work, a collaboration with Bonnie Berger's group at MIT, developed a deep-learning model to predict cancer-specific neutral mutation rates at kilobase-scale resolution from epigenomic annotations. Applying this model to the Pan-Cancer Analysis of Whole Genomes (PCAWG) resource identified potential new driver mutations in understudied... Read more about New preprint on learning patterns of somatic mutation in cancer

Whole-exome imputation paper published in Nature Genetics

July 5, 2021
Alison Barton's paper on whole-exome imputation and subsequent association and fine-mapping analyses in UK Biobank (Barton et al. 2021 Nat Genet) is now published -- congratulations, Alison! Imputation is a statistical approach that leverages genetic data from a reference panel to enable analysis of genetic variants that are not directly measured in a cohort, thereby expanding the utility of existing data sets without incurring additional cost.... Read more about Whole-exome imputation paper published in Nature Genetics

Two talks and two posters at ProbGen 2021

April 16, 2021
Our lab attended the Probabilistic Modeling in Genomics (ProbGen) 2021 virtual conference. Alison Barton and Maxwell Sherman spoke about their work on whole-exome imputation in UK Biobank (Alison) and deep-learning neutral somatic mutation rates in cancers (Max), and Margaux Hujoel and Ronen Mukamel presented posters on genotyping and association analysis of copy-number variants (Margaux) and variable number tandem repeats (Ronen).

New preprint on large-effect protein-coding repeat polymorphisms

January 20, 2021
We are excited to share a new preprint, "Protein-coding repeat polymorphisms strongly shape diverse human phenotypes" (Mukamel*, Handsaker* et al.), which finds that some of the largest effects of common genetic variants on human phenotypes arise from variable-number-of-tandem-repeat (VNTR) variation unseen by the analytical approaches used in large-scale human genetic studies. This exciting collaboration with Bob Handsaker and Steve McCarroll leveraged the initial... Read more about New preprint on large-effect protein-coding repeat polymorphisms

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