Germline and Somatic Microsatellite Genotypes in Pediatric Brain Tumors

Email Principal Investigator
Ongoing
Data
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Brian Rood

Children’s National Hospital
Washington, DC, USA

CBTN Data Used

Backer

Foundation grant and philanthropy

About this

Project

Microsatellites consist of a 1-6 base pair unit repeated in tandem to form an array. Over 600,000 unique microsatellites exist in the human genome, and are often embedded in gene introns, exons, and regulatory regions. Interestingly, the length of microsatellite loci frequently change due to strand slip replication and heterozygote instability, varying between alleles and between individuals. These changes can influence gene expression by inducing Z-DNA and H-DNA folding; altering nucleosome positioning; and changing the spacing of DNA binding sites. Non-coding variations can alter secondary structure and protein/RNA binding of the genes proximate to their locations, resulting in changes in transcriptional and translational activity as well as alternative splicing. Within exons, microsatellite loci lengths that are multiples of 3 and 6 often cause amino acid gain or loss by staying in sync with codon triplets; other non-modulo-3 lengths typically cause frameshift mutations

Numerous Genome-wide Associated Studies (GWAS) have focused on single nucleotide variants, ignoring non-coding regions or repetitive DNA. However, many studies have shown linkage between the length of repetitive DNA microsatellites and a number of neurological disorders such as Huntington disease and Friedreich ataxia; the former caused by a microsatellite variant in the coding sequence and the latter in a non-coding intronic sequence. In addition, recent studies have shown that microsatellite variations can contribute to the genetic background of several cancers.

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Scientists

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What are the goals of this project?

The goals of this project are to identify pediatric brain tumor associated microsatellite loci in germline DNA whose genotypes are correlated with the presence of disease, correlate microsatellite genotypes in germline DNA from tumor patients with paired tumor microsatellite genotype and to nalyze the effect of microsatellite genotype on tumor biology via transcription and splicing of proximate genes using RNA sequencing data

Specimen Data

The Children's Brain Tumor Network contributed to this project by providing access to the Pediatric Brain Tumor Atlas.

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