Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq

Genome Research
Yu KongJohn M Greally

Abstract

Current approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost, or the need to culture cells. We describe the mosaic aneuploidy detection by massively parallel sequencing (MAD-seq) capture assay and the MADSEQ analytical approach that allow low (<10%) levels of mosaicism for chromosomal aneuploidy or regional loss of heterozygosity to be detected, assigned to a meiotic or mitotic origin, and quantified as a proportion of the cells in the sample. We show results from a multi-ethnic MAD-seq (meMAD-seq) capture design that works equally well in populations of diverse racial and ethnic origins and how the MADSEQ analytical approach can be applied to exome or whole-genome sequencing data, revealing previously unrecognized aneuploidy or copy number neutral loss of heterozygosity in samples studied by the 1000 Genomes Project, cell lines from public repositories, and one of the Illumina Platinum Genomes samples. We have made the meMAD-seq capture design and MADSEQ analytical software open for unrestricted use, with the goal that they can be applied in clinical samples to allow new insights into the unrecognized prevalence of mosaic chromosomal aneuploidy in humans and its pheno...Continue Reading

References

Nov 6, 1998·Science·J A ThomsonJ M Jones
Apr 9, 1999·Archives of Disease in Childhood. Fetal and Neonatal Edition·V S Lestou, D K Kalousek
Dec 9, 2003·Nature Biotechnology·Jonathan S DraperPeter W Andrews
Dec 20, 2003·Nature·UNKNOWN International HapMap Consortium
Mar 25, 2006·Prenatal Diagnosis·Louise Wilkins-HaugCynthia C Morton
Oct 21, 2006·Laboratory Investigation; a Journal of Technical Methods and Pathology·Julie L RyanMargaret L Gulley
Nov 15, 2006·American Journal of Medical Genetics. Part a·Blake C BallifBassem A Bejjani
Dec 17, 2008·The Journal of Molecular Diagnostics : JMD·Angelique J A KooperArie P T Smits
Apr 9, 2009·American Journal of Medical Genetics. Part a·Aaron TheisenLisa G Shaffer
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jan 29, 2010·Blood·Christine O'KeefeJaroslaw P Maciejewski
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Apr 12, 2011·Nature Biotechnology·Seth M TaapkenKaren D Montgomery
May 3, 2011·Human Reproduction Update·Jannie van Echten-ArendsSjoerd Repping
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Dec 27, 2011·Fertility and Sterility·Matthew RabinowitzZachary Demko
Apr 25, 2012·Journal of the American Academy of Child and Adolescent Psychiatry·Sven SandinAbraham Reichenberg
May 9, 2012·Nature Genetics·Cathy C LaurieBruce S Weir
May 9, 2012·Nature Genetics·Kevin B JacobsStephen J Chanock
Nov 22, 2012·American Journal of Medical Genetics. Part a·Anna KostaneckaMary Pipan
Apr 6, 2013·Stem Cells and Development·Masood BazrgarHossein Baharvand
Apr 19, 2013·Nature Reviews. Genetics·Leslie G Biesecker, Nancy B Spinner
Mar 19, 2014·Methods in Molecular Biology·Francesca FaggioliCristina Montagna
May 31, 2014·PLoS Genetics·Esther R BerkoJohn M Greally
Sep 10, 2014·Proceedings of the National Academy of Sciences of the United States of America·Kristin A KnouseAngelika Amon
Mar 10, 2015·American Journal of Human Genetics·Mitchell J MachielaStephen J Chanock
Sep 19, 2015·Genome Biology·Stephane E CastelTuuli Lappalainen
Oct 4, 2015·Nature·UNKNOWN 1000 Genomes Project ConsortiumGonçalo R Abecasis
Jan 29, 2016·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Zirui DongZhengfeng Xu
Mar 5, 2016·American Journal of Human Genetics·Selina Vattathil, Paul Scheet

❮ Previous
Next ❯

Citations

Dec 16, 2020·Molecular Genetics & Genomic Medicine·Małgorzata RydzaniczRafał Płoski

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Revista medico-chirurgicală̆ a Societă̆ţ̜ii de Medici ş̧i Naturaliş̧ti din Iaş̧i
M Covic, T Angheloni
© 2022 Meta ULC. All rights reserved