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. 2021 Sep 20;2(4):100766.
doi: 10.1016/j.xpro.2021.100766. eCollection 2021 Dec 17.

Analytical protocol to identify local ancestry-associated molecular features in cancer

Jian Carrot-Zhang  1   2   3 , Seunghun Han  2   3 , Wanding Zhou  4   5 , Jeffrey S Damrauer  6 , Anab Kemal  7 ; Cancer Genome Atlas Analysis Network; Andrew D Cherniack  1   2   3 , Rameen Beroukhim  1   2   3   8   9
Collaborators, Affiliations

Analytical protocol to identify local ancestry-associated molecular features in cancer

Jian Carrot-Zhang et al. STAR Protoc. .

Abstract

People of different ancestries vary in cancer risk and outcome, and their molecular differences may indicate sources of these variations. Determining the "local" ancestry composition at each genetic locus across ancestry-admixed populations can suggest causal associations. We present a protocol to identify local ancestry and detect the associated molecular changes, using data from the Cancer Genome Atlas. This workflow can be applied to cancer cohorts with matched tumor and normal data from admixed patients to examine germline contributions to cancer. For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020).

Keywords: Bioinformatics; Cancer; Genomics.

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Conflict of interest statement

A.D.C. receives research funding from Bayer. R.B. owns equity in and consults for Scorpion and Ampressa Therapeutics and receives research funding from Novartis.

Figures

None
Graphical abstract
Figure 1
Figure 1
Analytical workflow for identifying local ancestry-associated molecular features in cancer Part 1: Preparation of TCGA and 1000 Genomes genotyping data; Part 2: Haplotype estimation and local ancestry assignments; Part 3: Examples of correlation analyses utilizing local ancestry information.
Figure 2
Figure 2
Accuracy assessment of local ancestry identification (A) Karyograms of six individuals from the TCGA cohort. Upper panel: none-admixed individuals from EUR, AFR and EAS populations, respectively. Lower panel: individuals with mixed ancestries. (B–D) (B) Correlation of global ancestry indicated by the proportions of EUR, (C) AFR and (D) EAS estimated from RFMix and ADMIXTURE. Upper panel: TCGA breast cancer cohort; Lower panel: TCGA prostate cancer cohort. r values are calculated from Pearson’s correlation.
See this image and copyright information in PMC

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