Laufey Amundadottir Ph.D.
|Organization:||National Cancer InstituteDivision of Cancer Epidemiology & Genetics, Laboratory of Translational Genomics|
|Address:||8717 Grovemont CircleATC Room 225C|
Dr. Amundadottir received a Ph.D. in Cell Biology in 1995 from Georgetown University in Washington, D.C. Her postdoctoral training was at the Department of Genetics at Harvard Medical School in Boston, MA. She joined deCODE genetics in Iceland in 1998 as the head of the Division of Cancer Genetics where she led genome wide linkage and association efforts in various cancers. Dr. Amundadottir joined the NCI in 2007 as a senior scientist and became an investigator in the Laboratory of Translational Genomics in 2008. Her current work focuses on genome wide association studies and functional characterization of plausible causal variants in order to understand how common sequence variation plays a role in the development of cancer.
Major advances have occurred in the last few years in our understanding of the genetics of common diseases, including cancer. Genome wide association studies (GWAS), which assess hundreds of thousands of single nucleotide polymorphisms (SNPs) in large cohort or case-control studies have provided new insights into the genomic regions that alter an individual’s risk of developing cancer. These efforts have led to the discovery of multiple common risk variants for several types of common cancer. However, the elucidation of functional roles for these variants with respect to disease is in the very early stages. This interface between genetics and the functional studies that follow suit is of special interest to the laboratory. Our approach focuses on the molecular phenotypes of association findings and functional characterization of plausible causal variants in order to understand how common sequence variation plays a role in the development of cancer. Work in the laboratory involves association analysis of large datasets, deep sequencing of candidate regions for fine mapping, genome wide and targeted expression profiling, gene regulation and epigenetics; and data analysis using current bioinformatics and statistical approaches.
PanScan is a GWAS of pancreatic cancer conducted within the framework of the NCI-sponsored Cohort Consortium and the Pancreatic Cancer Case Control Consortium (PANC4). The aim of the study is to identify common susceptibility variants for pancreatic cancer. Two GWAS phases have already been performed in 4,000 cases and 4,000 controls from 12 prospective cohort studies and 8 case control studies. This work resulted in the discovery of four susceptibility loci for pancreatic cancer on chromosomes 1q32.1 (NR5A2), 5p15.33 (TERT-CLPTM1L region), 9q34.2 (ABO) and 13q22.1 (nongenic). A third GWAS phase with an additional 2,000 cases is in progress. My laboratory conducts fine mapping of risk loci identified in PanScan as well as functional studies with the aim of finding the underlying functional variants and understanding the mechanism by which they increase risk of cancer. This works involves statistical approaches (imputation), genomics (RNA-seq, ChIP-seq, MeDIP-chip) and more focused functional approaches within each risk locus targeting specific genes and molecular phenotypes to connect risk variants to molecular phenotypes that can explain the underlying risk.
Genome wide association studies have successfully identified risk variants for prostate cancer at over 45 loci and many have been unambiguously replicated in several populations. One of these loci is on chromosome 19q13.33 in the KLK3 gene that encodes prostate specific antigen or PSA. Using next generation sequencing we have fine mapped the KLK3 locus on chromosome 19q13.33 to a set of three highly correlated SNPs within the KLK3 gene. The major alleles at these three SNPs were associated with an increased risk of nonaggressive prostate cancer as well as increased PSA levels in control subjects, indicating that these variants may influence the development or diagnosis of nonaggressive prostate cancer, potentially due to differential case identification related to PSA levels. We are currently in the process of expanding our studies on the genetics of PSA levels and its relationship to prostate cancer within PEGASUS, a GWAS of prostate cancer and related phenotypes conducted within the Cancer Genetic Markers of Susceptibility (CGEMS) study using a 2.5 million SNP genotyping platform.
Prostate cancer GWAS studies have not implicated the Y chromosome in the risk of prostate cancer, possibly because very few Y chromosome markers are represented on the genotyping platforms currently used. Although gene poor, there is evidence that loci on the Y chromosome may play a role in altering risk of cancer. Loss of this chromosome is one of the most common genetic alterations seen in prostate cancer and altered expression of genes residing on the Y chromosome has been reported in prostate cancer. Because most of the Y chromosome does not recombine, it is passed down unchanged from father to son through the generations. The only new changes introduced into the DNA sequence are from mutations. A set of biallelic markers can thus be used to identify Y chromosome haplogroups (or lineages) which can be organized along a phylogenetic tree and tested for association to disease. My laboratory is currently investigating the role of Y chromosome variation in prostate cancer risk using a set of SNPs that tag the most common European haplogroups. Prostate cancer cases and controls from five cohort studies are included in the study totaling approximately 5,000 cases and 5,000 controls.
Member of PanScan: http://epi.grants.cancer.gov/PanScan/
Irene Collins, Ph.D. (Biologist/Lab Manager)