Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

By F. Favero, T. Joshi, A. Marquard, Nicolai J. Birkbak, M. Krzystanek, Qiyuan Li, Zoltán Szállási, A. Eklund. Annals of Oncology, 2014

735 citations recorded by the source corpus.

We describe our algorithm and software for determining copy number profiles from tumor genome sequencing data, and find that it compares favorably to existing algorithms for the same purpose.

Subfields: Cancer Research, Genetics, Pathology and Forensic Medicine

View Paper: https://www.semanticscholar.org/paper/b3d5c97287522c6b6036db184a41219034609a0a

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

1. Nicholas McGranahan
2. Victor E. Velculescu
3. S. Baylin
4. D. Pardoll
5. Charles Swanton

In Genetics

1. S. Baylin
2. Javier Herrero
3. Rachel Karchin
4. Christophe Dessimoz
5. James Robert White
6. Nicholas McGranahan
7. Manel Esteller

In Pathology and Forensic Medicine

1. S. Baylin
2. D. Pardoll

Citations in the corpus

• Pan-tumor genomic biomarkers for PD-1 checkpoint blockade–based immunotherapy (2018, positive): “Allele-specific copy number and purity estimation VarScan2 (55) output copy number ratio and SNP were input to Sequenza (56) to provide a maximum a posteriori estimation for cellularity and segmented allele-specific copy number for each sample.”
• Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma (2017, methodology): “0.22 (68) to determine regions of significant focal copy-number alterations, using ASCAT/Sequenza’s inferred copy-number segments, and associated copynumber values were defined as log2 of the segment’s relative copy-number.”
• Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer (2016, methodology): “To validate the accuracy of our method to estimate tumor purity we compared tumor purity estimates derived by SCHISM to four methods of estimating purity: 1) Pathology review, 2) Mutation allele frequency, 3) PyLOH (49) and 4) Sequenza (50) (Supplementary Table S18).”
• Primary resistance to PD-1 blockade mediated by JAK1/2 mutations (2016, methodology): “Local tumor Copy Number (CNt,) Tumor Fraction (purity, or p) and Stromal Fraction (1-p) were produced by Sequenza (44), which uses both depth-ratio and SNP minor B-allele frequencies to estimate tumor ploidy, percent tumor content and perform allele-specific copy number variation analysis.”
• Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution (2017, methodology): “…themajority of copy-number tools rely on the relative coverage and variant allele frequency of single nucleotide polymorphisms (SNPs) in the tumor and matched normal across the genome or exome (Carter et al., 2012; Favero et al., 2015; Ha et al., 2014; Shen and Seshan, 2016; Van Loo et al., 2010).”
• Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma (2016, positive): “Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.”