Using existing pediatric cancer data from the Gabriella Miller Kids First Data Resource Program

Childhood cancer and birth defects are leading causes of childhood mortality, and studies suggest that birth defects increase pediatric cancer risk. The Gabriella Miller Kids First Pediatric Research Program (Kids First) seeks to alleviate these conditions by building an expansive resource of genetic and clinical data from patients with pediatric cancer and birth defects and their families. This article describes the data and support provided by the Kids First Data Resource Center and the Kids First Data Resource Center Data Resource Portal, which enables the public to review Kids First studies and request access to individual data. The Kids First Portal contains data from more than 34 000 participants and connects with CAVATICA (Seven Bridges Genomics, Inc, now part of Velsera), a cloud-based analysis and sharing platform. Researchers have used Kids First data to investigate a variety of cancers and further funding opportunities are available. The Kids First Portal is a unique resource that unites pediatric cancer and birth defects to uncover their genetic etiology and improve patients' lives.

Abstract 2589: Identifying cancer susceptibility variants and genes using whole exome and genome sequencing: a literature review

The application of Next Generation Sequencing (NGS) technologies in cancer research enabled the discovery of novel somatic mutations at an unprecedented speed through efficient high-throughput profiling of DNA variation in tumor samples. In contrast, the identification through NGS studies of germline variation associated with cancer has been more difficult and with limited consensus around best practices for study design and analytical techniques. We performed a review of the 2005-2016 PubMed English literature for genome-wide germline sequencing studies that were aimed at identifying new cancer susceptibility genes or variants. We extracted and summarized the experimental and analytical designs, methods and tools implemented in the selected literature together with their degree of success and limitations in identifying cancer susceptibility variants. About 80 in-scope publications were identified and examined in depth. The most studied cancer types were colorectal, breast, blood and lung and were investigated predominantly via whole exome sequencing (primarily using Illumina HiSeq) in familial cases of Caucasian ethnicity. Only 10 studies used whole genome sequencing and 15 adopted a case control study design. A large fraction of the familial studies was limited to 1 or 2 families and sequenced 2 or less cases per family. Reporting of key data quality information (e.g., human sequence coverage) was inconsistent throughout the publications. While the methods for sequence alignment and variant calling converged towards those implemented in established bioinformatic tools (e.g., BWA, GATK), there were no standard approaches for filtering or prioritizing of variants. Most studies included some degree of technical validation, often restricted to the top few variants or genes. About 60% of the studies included replication in an independent group of cancer patients and 55% functionally validated their findings to some extent. Our work provides valuable data and insights to inform future sequencing studies of cancer genetic susceptibility, and points to the need for improving standardization and completeness in reporting of quality control metrics, study design rationale and interpretation of findings.

Citation Format: Melissa Rotunno, Mindy Clyne, Tram Lam, Leah Mechanic, Danielle Daee, Stefanie Nelson, Elizabeth Gillanders, Alisa Goldstein. Identifying cancer susceptibility variants and genes using whole exome and genome sequencing: a literature review [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2589. doi:10.1158/1538-7445.AM2017-2589

A histone-fold complex and FANCM form a conserved DNA-remodeling complex to maintain genome stability

FANCM remodels branched DNA structures and plays essential roles in the cellular response to DNA replication stress. Here, we show that FANCM forms a conserved DNA-remodeling complex with a histone-fold heterodimer, MHF. We find that MHF stimulates DNA binding and replication fork remodeling by FANCM. In the cell, FANCM and MHF are rapidly recruited to forks stalled by DNA interstrand crosslinks, and both are required for cellular resistance to such lesions. In vertebrates, FANCM-MHF associates with the Fanconi anemia (FA) core complex, promotes FANCD2 monoubiquitination in response to DNA damage, and suppresses sister-chromatid exchanges. Yeast orthologs of these proteins function together to resist MMS-induced DNA damage and promote gene conversion at blocked replication forks. Thus, FANCM-MHF is an essential DNA-remodeling complex that protects replication forks from yeast to human.