Leland Stanford Junior University

Giwon Shin

Hanlee P Ji

Billy Tsz Cheong Lau

HoJoon Lee

A method for determining if a tumor has a mutation in a microsatellite is provided. In some embodiments, the method may comprise: (a) isolating genomic DNA from a tumor sample and a non-tumor sample from the same patient to produce: i. a sample of tumor DNA and ii. a sample of non-tumor DNA, respectively, (b) without pre-amplifying the tumor or non-tumor DNA, sequencing a plurality of microsatellite loci from both the tumor and non-tumor DNA using OS-seq to provide sequence reads, wherein the sequenced microsatellite loci comprise mononucleotide, dinucleotide, trinucleotide and tetranucleotide microsatellites loci, and (c) comparing the results.

Method for determining if a tumor has a mutation in a microsatellite

A method for analyzing short tandem repeats (STRs) is described herein. In some embodiments, the method comprises: separately digesting two portions of a genomic sample at sites that are upstream and downstream of an STR; fragmenting those products; ligating adaptors to the fragmentation products; selectively amplifying part of the top strand but not the bottom strand of the ligation products derived from the first portion, and part of the bottom strand but not the top strand of the ligation products derived from the second portion; sequencing at least some of the amplification products to produce a plurality of top strand reads and a plurality of bottom strand reads; and counting the number of STR repeats in a sequence read. A kit for performing the method is also provided.

Growing community of inventors

Stanford, CA, United States of America

Giwon Shin