Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device.

PLoS One

Fluidigm Corporation, South San Francisco, California, United States of America.

Published: August 2008

Copy Number Variations (CNVs) of regions of the human genome have been associated with multiple diseases. We present an algorithm which is mathematically sound and computationally efficient to accurately analyze CNV in a DNA sample utilizing a nanofluidic device, known as the digital array. This numerical algorithm is utilized to compute copy number variation and the associated statistical confidence interval and is based on results from probability theory and statistics. We also provide formulas which can be used as close approximations.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483940PMC
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002876PLOS

Publication Analysis

Top Keywords

copy number
12
number variation
8
dna sample
8
nanofluidic device
8
mathematical analysis
4
analysis copy
4
variation dna
4
sample digital
4
digital pcr
4
pcr nanofluidic
4

Similar Publications

Recent single-cell experiments that measure copy numbers of over 40 proteins in individual cells at different time points [time-stamped snapshot (TSS) data] exhibit cell-to-cell variability. Because the same cells cannot be tracked over time, TSS data provide key information about the time-evolution of protein abundances that could yield mechanisms that underlie signaling kinetics. We recently developed a generalized method of moments (GMM) based approach that estimates parameters of mechanistic models using TSS data.

View Article and Find Full Text PDF

Changes in the copy number of large genomic regions, termed copy number variations (CNVs), contribute to important phenotypes in many organisms. CNVs are readily identified using conventional approaches when present in a large fraction of the cell population. However, CNVs that are present in only a few genomes across a population are often overlooked but important; if beneficial under specific conditions, a de novo CNV that arises in a single genome can expand during selection to create a larger population of cells with novel characteristics.

View Article and Find Full Text PDF

Cryo-EM structure of the conjugation H-pilus reveals the cyclic nature of the TrhA pilin.

bioRxiv

December 2024

Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, UK.

Conjugation, the major driver of the spread of antimicrobial resistance genes, relies on a conjugation pilus for DNA transfer. Conjugative pili, such as the F-pilus, are dynamic tubular structures, composed of a polymerized pilin, that mediate the initial donor-recipient interactions, a process known as mating pair formation (MPF). IncH are low-copy-number plasmids, traditionally considered broad host range, which are found in bacteria infecting both humans and animals.

View Article and Find Full Text PDF

Introduction: Structural variants (SVs) of the nebulin gene ( ), including intragenic duplications, deletions, and copy number variation of the triplicate region, are an established cause of recessively inherited nemaline myopathies and related neuromuscular disorders. Large deletions have been shown to cause dominantly inherited distal myopathies. Here we provide an overview of 35 families with muscle disorders caused by such SVs in .

View Article and Find Full Text PDF

Background And Aims: Familial hypercholesterolemia (FH) and other disorders with similar features are common genetic disorders that remain underdiagnosed and undertreated, due in part to the cost of screening. The aim of this study was to design and implement a whole gene targeted NGS panel for the molecular diagnosis of FH and statin intolerance with an emphasis on high quality variant calling, including copy number analysis.

Methods: A whole gene panel for hybridisation-based short read NGS was designed for the dominant FH-genes low density lipoprotein receptor (), apolipoprotein B (APOB), proproteinconvertas subtilisin/kexin type 9 (PCSK9), apolipoprotein E (APOE) and the recessive FH-genes low density lipoprotein receptor adaptor protein 1 (), ATP binding cassette subfamily member 5/8 (ABCG5/8) and lipase A, lysosomal acid type (), as well as solute carrier organic anion transporter family member 1B1 (), not an FH gene but linked to statin intolerance.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!