Research

Tracing lineages and studying human development

Tracing cell lineages is fundamental for understanding the rules governing how multicellular organisms develop. It's also key to describing complex biological processes involving the differentiation of multiple cell types with distinct lineage hierarchies. In humans, experimental lineage tracing isn't ethical. Instead, the Somatic Mutations in Development and Aging Lab relies on natural mutation markers created within cells as they proliferate and age.

Dr. Abyzov's lab has demonstrated that it is possible to trace lineages in healthy, noncancerous cells using natural variations in the nuclear and mitochondrial DNA. The lab is studying lineage ancestry in the earliest stages of human development.

The scientific community also is on the verge of being able to make a full and detailed cell lineage map of human embryonic and fetal development. The Somatic Mutations in Development and Aging Lab aims to contribute to that knowledge.

CNV and CNA analysis

Copy number variations (CNVs) in genomes are complex phenomena that aren't completely understood. Somatic copy number alterations (CNAs) are frequent in cancers. Researchers have tied CNAs to cancer susceptibility, progression and invasiveness. CNAs also are related to individual response to treatment and a patient's quality of life after treatment.

Detecting CNVs and CNAs is important to address a wide spectrum of clinical and scientific questions. Research in the Somatic Mutations in Development and Aging Lab focuses on discovering and analyzing CNVs and CNAs and understanding their relevance to diseases. The lab has developed and continues to improve a method — CNVnator and CNVpytor — to discover CNVs and perform genotyping from a read-depth analysis of personal genome or cancer sequencing.

Single-cell studies

Single-cell sequencing is the best way to study somatic mosaicism in healthy tissues and cancer. But due to the scarcity of DNA in a single cell, an amplification process is required. Clonal expansion can achieve such amplifications.

During amplification, a single cell is cultured to produce a colony. In in vitro, whole-genome amplification, DNA is amplified using polymerases.

The Abyzov Lab formulates strategies to control the quality of whole-genome amplification and to distinguish signal from noise that may be introduced during cell culture or DNA amplification. The lab also is working to create approaches to estimate the contributions of signal and noise when they can't be clearly distinguished.

Variant function

Simultaneous advances in genomics provide opportunities to study the origins and consequences of genomic variants. These advances include variant discovery and epigenomics, as well as functional genomics, including the emergence of these techniques:

• Chromatin immunoprecipitation sequencing (ChiP-seq).
• Assay for transposase-accessible chromatin with sequencing (ATAC-seq).
• High-throughput chromosome conformation capture (Hi-C).
• RNA sequencing (RNA-seq).

Various epigenomic properties predispose mutational processes to generate single nucleotide variation and structural variation. Inversely, germline and somatic variants affect genome function. But because many of those variants occur in noncoding regions of the genome, their effects aren't well understood. In response, the lab is working to clarify such effects, particularly focusing on variants contributing to neurodevelopmental conditions. These conditions include autism spectrum disorder and Tourette syndrome.

Cancer genomics

Over the past decade, high-throughput, next-generation technologies, coupled with computational algorithms, have helped scientists better understand the biology of cancer as well as the molecular underpinnings of cancer development and progression. Researchers have found numerous functionally significant point mutations and structural alterations in several types and subtypes of cancers. These alterations illustrate the diverse landscape of the cancer genome.

Dr. Abyzov's lab discovers and analyzes somatic point mutations and structural alterations in colon cancer and glioma. This includes deletions, duplications and copy number changes. The lab investigates the relationship between patterns of genetic alterations and modes of evolution of cancer, as well as molecular differences between cancer-free and cancer-adjacent polyps.

Analysis of mosaic variations in humans

Mutations in DNA that accumulate during each person's life span result in what are called mosaic bodies. In these bodies, each cell has unique variants in the genome. That phenomenon is called somatic mosaicism.

Despite the prevalence of somatic mosaicism, the lack of means to detect such variants at the level of single cells has limited study on this topic. But the dropping price of sequencing and recent advances in single-cell genomics now make such research possible.

Dr. Abyzov's lab is creating computational methods to precisely detect somatic mosaic variants by harnessing new experimental approaches. These approaches include clonal expansion and whole-genome amplification. By applying these approaches to human samples, the lab aims to answer questions about the origin, spread and consequence of mosaic mutations. These questions involve determining mutation rates, differences in the number and pattern of mutations between tissues and ages, as well as relevance of the mutation to diseases and aging.

The lab is part of the National Institutes of Health's Somatic Mosaicism Across Human Tissues Network.