Inferring Phenotypes of Copy Number Clones in Cancer Populations Using TreeAlign.

Hongyu Shi, Matthew Zatzman, Sohrab Shah, Andrew McPherson

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

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0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

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5 · Who and what money

Authors and funding

4 authors.

Hongyu ShiComputational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Matthew ZatzmanComputational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Sohrab ShahComputational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Andrew McPhersonComputational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. mcphera1@mskcc.org.

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026

$347.4M

NCI NIH HHS P30 CA008748

6 · The paper itself

Abstract

Somatic copy number changes modify gene expression and drive cancer development and progression. Single-cell techniques now allow for the profiling of both gene expression and copy number, opening the possibility of linking expression changes with copy number changes at a single-cell level. However, joint measurement of both expression and copy number from the same cell is not commonplace, and thus joint analysis of expression and copy number requires computational integration of the two modalities. TreeAlign is a method for matching cells in single-cell RNA (scRNA) data to clones inferred from single-cell whole genome sequence (scWGS) data. TreeAlign is phylogeny aware and capable of robustly modeling the effect of gene dosage on gene expression. In this chapter, we provide a practical guide for using TreeAlign to jointly analyze copy number and gene expression from single-cell whole genome sequencing and single-cell RNA sequencing datasets.

Indexed as

Computational BiologyDNA Copy Number VariationsGene DosageNeoplasmsSingle-Cell AnalysisSoftwareAlgorithmsGene Expression ProfilingGene Expression Regulation, NeoplasticHumansPhenotypeWhole Genome SequencingCancer genomicsProbabilistic modelingSingle-cell RNA sequencingSingle-cell whole genome sequencingTumor evolutionTumor microenvironment

Identifiers

PMID40779108

DOI10.1016/j.cell.2016.11.022

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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.