April Shu, a postdoc in Chung and Shen labs, has accepted a faculty position in Population and Public Health Sciences at USC. Congratulations April!

We have been awarded a 5-year Maximizing Investigators’ Research Award (MIRA) R35 grant from NIGMS. We proposed to develop computational methods to interpret coding and noncoding variation in genetic analysis, including risk gene discovery, population screening, and clinical genetic testing. A key idea is to conceptually separate the impact of genetic variation at molecular (protein function and expression) and population (selection coefficient) levels, and jointly estimate them using probalistic graphical models and deep learing. To do that, we will use large human population genome sequence data, protein structure, and functional genomics data. New postdoc positions to work on this project are available.

Our team has been awarded a 3-year SFARI grant. We will study the functional impact of genetic mutations in autism risk genes using deep mutational scan, machine learning, and biophysical modeling. This grant is a collaboration with Brian O’Roak lab at OHSU and Jake Michaelson lab at University of Iowa.

Xiao Fan, an associate research scientist in Chung and Shen labs, has accepted a faculty position in Department of Biomedical Engineering at University of Florida. Congratulations Xiao!

Her lab (https://xiaofan-lab.github.io) will open in Jan 2023. She is recruiting students and postdocs.

Sep 2022

Our team has been awarded a new Autism Center of Excellence (ACE) grant. We will study the development trajectory of children who are at risk of developmental disorders due to highly penetrant genetic factors. The families will be recruited from GUARDIAN, a separate study on newborn screening by whole genome sequencing. Our team will lead the computational and statistical analysis of genomic data.

Our work on genetic causes of autism is recently published as Zhou et al., 2022 on Nature Genetics. Congratulations to Xueya, April, Joseph, and our collaborators at Columbia and the SPARK consortium.

In the paper, we described the analysis of more than 40,000 autism cases to quantify contribution of de novo and rare genetic variants to autism. We confirmed many previously discovered risk genes and found several new risk genes. One of the most notable results is that a few new risk genes, such as NAV3, contribute to autism risk mostly through rare variants inherited from parents that mostly do not have diagnosed autistic conditions. These rare inherited variants have significant but moderate risk, supporting the nature of autism genetic risk is often complex and multi-factorial – often called as oligo-genic or poly-genic.

Chloe Williams wrote a report on our work on Spectrum : Scans of sundry variant types uncover autism-linked genes.

We welcome new summer students: Lily, Demi, Maugaux, Lesi, and Arthur.

Xiao received a K99/R00 award from NIH! She proposed to develop new statistical and computational methods to improve interpretation of genetic variants in human genetics studies and clinical diagnosis. Congratulations Xiao!