ArticleGenome research2013
Haplotype-based profiling of subtle allelic imbalance with SNP arrays.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Patterns and drivers of 43,617 mosaic chromosomal alterations in blood.Nature genetics · 2026Article
- Genetic drivers and clinical consequences of mosaic chromosomal alterations in 1 million individuals.medRxiv : the preprint server for health sciences · 2025Article
- Impact of cancer therapy on clonal hematopoiesis mutations and subsequent clinical outcomes.Blood advances · 2024Article
- A pan-tissue survey of mosaic chromosomal alterations in 948 individuals.Nature genetics · 2023Article
- Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing.Nature genetics · 2023Article
- Schizophrenia-associated somatic copy-number variants from 12,834 cases reveal recurrentCell genomics · 2023Article
- Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes.Nature biotechnology · 2023Article
- Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing.Nucleic acids research · 2022Article
- Prevalence of cancer susceptibility variants in patients with multiple Lynch syndrome related cancers.Scientific reports · 2021Article
- Deciphering the genetic and epidemiological landscape of mitochondrial DNA abundance.Human genetics · 2021Article
- Pan cancer patterns of allelic imbalance from chromosomal alterations in 33 tumor types.Genetics · 2021Article
- Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity.Genome biology · 2020Article
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- Article
- Large-scale analysis of acquired chromosomal alterations in non-tumor samples from patients with cancer.Nature biotechnology · 2020Article
- Driver Mutations in Normal Airway Epithelium Elucidate Spatiotemporal Resolution of Lung Cancer.American journal of respiratory and critical care medicine · 2019Article
- Directional allelic imbalance profiling and visualization from multi-sample data with RECUR.Bioinformatics (Oxford, England) · 2019Article
- Genomic landscape of allelic imbalance in premalignant atypical adenomatous hyperplasias of the lung.EBioMedicine · 2019Article
- System for Quality-Assured Data Analysis: Flexible, reproducible scientific workflows.Genetic epidemiology · 2019Article
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Authors and funding
2 authors.
Funding
Abstract
Due to limitations of surgical dissection and tumor heterogeneity, tumor samples collected for cancer genomics studies are often heavily diluted with normal tissue or contain subpopulations of cells harboring important aberrations. Methods for profiling tumor-associated allelic imbalance in such scenarios break down at aberrant cell proportions of 10%-15% and below. Here, we present an approach that offers a vast improvement for detection of subtle allelic imbalance, or low proportions of cells harboring aberrant allelic ratio among nonaberrant cells, in unpaired tumor samples using SNP microarrays. We leverage the expected pattern of allele-specific intensity ratios determined by an individual's germline haplotypes, information that has been ignored in existing approaches. We demonstrate our method on real and simulated data from the CRL-2324 breast cancer cell line genotyped on the Illumina 370K array. Assuming a 5 million SNP array, we can detect the presence of aberrant cells in proportions lower than 0.25% in the breast cancer sample, approaching the sensitivity of some minimal residual disease assays. Further, we apply a hidden Markov model to identify copy-neutral LOH (loss of heterozygosity) events as short as 11 Mb in mixtures of only 4% tumor using 370K data. We anticipate our approach will offer a new paradigm for genomic profiling of heterogeneous samples.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.