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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France; 4Institut Universitaire de France (IUF), 75231 Paris Cedex 05, France ↵5 These authors contributed equally to this work. Corresponding author: dgresham@nyu.eduAbstractCopy number variants (CNVs), duplications and deletions of genomic...
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Erratum: Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy
- Edward F. Attiyeh,
- Sharon J. Diskin,
- Marc A. Attiyeh,
- Yaël P. Mossé,
- Cuiping Hou,
- Eric M. Jackson,
- Cecilia Kim,
- Joseph Glessner,
- Hakon Hakonarson,
- Jaclyn A. Biegel,
- and John M. Maris
Genome Res. March 2009 19: 520
....M John Maris Jaclyn Biegel Marc Attiyeh Attiyeh, Edward F Mossé, YP Mossé EF Attiyeh Maris, J genome;19/3/520 1088-9051 Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy Genomic copy number...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...essentially performs feature selection alongside the main regression task.Deep learningRecently, deep learning–based AI technologies have been introduced into genomic data analysis. Deep learning is based on DNNs, which are constructed from multiple layers of interconnected neurons. Fundamentally, each...
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Research: Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling
- Lu Liu,
- He Chen,
- Cheng Sun,
- Jianyun Zhang,
- Juncheng Wang,
- Meijie Du,
- Jie Li,
- Lin Di,
- Jie Shen,
- Shuang Geng,
- Yuhong Pang,
- Yingying Luo,
- Chen Wu,
- Yusi Fu,
- Zhe Zheng,
- Jianbin Wang,
- and Yanyi Huang
Genome Res. January 2022 32: 44-54; Published in Advance December 28, 2021, doi:10.1101/gr.275453.121
...chromosomes, but with a 2.4% (n = 498) cellular occurrence rate, it can be easily missed if the experimental throughput is not large enough. We verified low-frequency autosomal aneuploidy using fluorescence in situ hybridization assays and quantitatively confirmed the copy number gains and losses in Chr 3, 8...
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Method: Copy number variation detection and genotyping from exome sequence data
- Niklas Krumm,
- Peter H. Sudmant,
- Arthur Ko,
- Brian J. O'Roak,
- Maika Malig,
- Bradley P. Coe,
- NHLBI Exome Sequencing Project,
- Aaron R. Quinlan,
- Deborah A. Nickerson,
- and Evan E. Eichler
Genome Res. August 2012 22: 1525-1532; Published in Advance May 14, 2012, doi:10.1101/gr.138115.112
..., USA Abstract While exome sequencing is readily amenable to single-nucleotide variant discovery, the sparse and nonuniform nature of the exome capture reaction has hindered exome-based detection and characterization of genic copy number variation. We developed a novel method using singular...
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Research: De novo rates and selection of large copy number variation
- Andy Itsara,
- Hao Wu,
- Joshua D. Smith,
- Deborah A. Nickerson,
- Isabelle Romieu,
- Stephanie J. London,
- and Evan E. Eichler
Genome Res. November 2010 20: 1469-1481; Published in Advance September 14, 2010, doi:10.1101/gr.107680.110
...neurocognitive disease. We show that a significant limitation in directly measuring genome-wide CNV mutation is accessing DNA derived from primary tissues as opposed to cell lines. We conservatively estimated the genome-wide CNV mutation rate using single nucleotide polymorphism (SNP) microarrays to analyze...
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Methods: High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping
- Daniel A. Peiffer,
- Jennie M. Le,
- Frank J. Steemers,
- Weihua Chang,
- Tony Jenniges,
- Francisco Garcia,
- Kirt Haden,
- Jiangzhen Li,
- Chad A. Shaw,
- John Belmont,
- Sau Wai Cheung,
- Richard M. Shen,
- David L. Barker,
- and Kevin L. Gunderson
Genome Res. September 2006 16: 1136-1148; Published in Advance August 9, 2006, doi:10.1101/gr.5402306
...measurement of both signal intensity variations and changes in allelic composition makes it possible to detect both copy number changes and copy-neutral loss-of-heterozygosity (LOH) events. We demonstrate the utility of SNP-CGH with two Infinium whole-genome genotyping BeadChips, assaying 109,000 and 317...
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LETTER: Copy number variation at the 7q11.23 segmental duplications is a susceptibility factor for the Williams-Beuren syndrome deletion
- Ivon Cuscó,
- Roser Corominas,
- Mònica Bayés,
- Raquel Flores,
- Núria Rivera-Brugués,
- Victoria Campuzano,
- and Luis A. Pérez-Jurado
Genome Res. May 2008 18: 683-694; Published in Advance February 21, 2008, doi:10.1101/gr.073197.107
...and availability of scanning technologies such as microarray-based comparative genomic hybridization, paired-end clone sequencing, computational approaches, and high-throughput single-nucleotide polymorphism genotyping have facilitated detection of previously unrecognized sub-microscopic structural variants...
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Research: Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma
- Gonzalo Lopez,
- Karina L. Conkrite,
- Miriam Doepner,
- Komal S. Rathi,
- Apexa Modi,
- Zalman Vaksman,
- Lance M. Farra,
- Eric Hyson,
- Moataz Noureddine,
- Jun S. Wei,
- Malcolm A. Smith,
- Shahab Asgharzadeh,
- Robert C. Seeger,
- Javed Khan,
- Jaime Guidry Auvil,
- Daniela S. Gerhard,
- John M. Maris,
- and Sharon J. Diskin
Genome Res. September 2020 30: 1228-1242; Published in Advance August 13, 2020, doi:10.1101/gr.252106.119
...polymorphism (SNP) genotyping and comparative genomic hybridization (CGH) arrays. More recently, these approaches were adapted and applied to read-depth measures from high-throughput sequencing. Numerous segmentation algorithms exist for both array (Carter 2007) and sequence-based (Zhao et al. 2013) approaches...
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Research: Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion
- Brittany L. Daughtry,
- Jimi L. Rosenkrantz,
- Nathan H. Lazar,
- Suzanne S. Fei,
- Nash Redmayne,
- Kristof A. Torkenczy,
- Andrew Adey,
- Melissa Yan,
- Lina Gao,
- Byung Park,
- Kimberly A. Nevonen,
- Lucia Carbone,
- and Shawn L. Chavez
Genome Res. March 2019 29: 367-382; Published in Advance January 25, 2019, doi:10.1101/gr.239830.118
..., cleavage-stage embryos (N = 50) were disassembled into individual blastomeres, cellular fragments, and polar bodies if still present (Fig. 1C) for chromosomal copy number variation (CNV) analysis and single-nucleotide polymorphism (SNP) genotyping. Another subset of intact embryos (N = 25) between...

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