DOI: 10.1101/488601Dec 7, 2018Paper

Uncovering missed indels by leveraging unmapped reads

BioRxiv : the Preprint Server for Biology
Mohammad Shabbir HasanLiqing Zhang

Abstract

In current practice, Next Generation Sequencing (NGS) applications start with mapping/aligning short reads to the reference genome, with the aim of identifying genetic mutations. While most short reads can be mapped to the reference genome accurately by existing alignment tools, a significant number remain unmapped and excluded from downstream analyses thus potentially discarding important biological information hidden in the unmapped reads. This paper describes Genesis-indel, a computational pipeline that explores the unmapped reads to identify novel indels that are initially missed in the alignment procedure. Genesis-indel is applied to the unmapped reads of 30 Breast Cancer patients from TCGA. Results show that the unmapped reads are conserved between the two subtypes of breast cancer investigated in this study and might contribute to the divergence between the subtypes. Genesis-indel is able to leverage the unmapped reads to identify 72,997 small to large novel high-quality indels previously not found in the original alignments and among them, 16,141 have not been annotated in the widely used mutation database. Statistical analysis shows that these new indels mostly altered the oncogenes and tumor suppressor genes. Function...Continue Reading

Related Concepts

Malignant Neoplasm of Breast
Carcinoma
Genes
Genome
Oncogenes
Computer Software
Tumor Suppressor Genes
Subtype (Attribute)
Downstream
Carcinogenesis

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Breast Cancer: Risk Factors

Breast cancer is a multifactorial disease that is influenced by both environmental and genetic factors. Discover the latest research on the environmental and genetic risk factors for breast cancer here.

Related Papers

Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme
K TakitaY Nakamura
Nihon rinsho. Japanese journal of clinical medicine
T Ichikawa
Annals of Oncology : Official Journal of the European Society for Medical Oncology
E Anderson, T Howell
© 2021 Meta ULC. All rights reserved