scholarly journals Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

2008 ◽  
Vol 18 (12) ◽  
pp. 1865-1874 ◽  
Author(s):  
P. M. Kim ◽  
H. Y.K. Lam ◽  
A. E. Urban ◽  
J. O. Korbel ◽  
J. Affourtit ◽  
...  
Keyword(s):  
Human Genome ◽  
Copy Number ◽  
Evolutionary History ◽  
Copy Number Variants ◽  
Segmental Duplications

scholarly journals Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils

PLoS Biology ◽  
2020 ◽  
Vol 18 (11) ◽  
pp. e3000926 ◽  
Author(s):  
Young Mi Kwon ◽  
Kevin Gori ◽  
Naomi Park ◽  
Nicole Potts ◽  
Kate Swift ◽  
...  
Keyword(s):  
Positive Selection ◽  
Cancer Cells ◽  
Cell Lines ◽  
Copy Number ◽  
Convergent Evolution ◽  
Evolutionary History ◽  
Genome Instability ◽  
Copy Number Variants ◽  
Tasmanian Devil ◽  
Transmissible Cancer

Devil facial tumour 1 (DFT1) is a transmissible cancer clone endangering the Tasmanian devil. The expansion of DFT1 across Tasmania has been documented, but little is known of its evolutionary history. We analysed genomes of 648 DFT1 tumours collected throughout the disease range between 2003 and 2018. DFT1 diverged early into five clades, three spreading widely and two failing to persist. One clade has replaced others at several sites, and rates of DFT1 coinfection are high. DFT1 gradually accumulates copy number variants (CNVs), and its telomere lengths are short but constant. Recurrent CNVs reveal genes under positive selection, sites of genome instability, and repeated loss of a small derived chromosome. Cultured DFT1 cell lines have increased CNV frequency and undergo highly reproducible convergent evolution. Overall, DFT1 is a remarkably stable lineage whose genome illustrates how cancer cells adapt to diverse environments and persist in a parasitic niche.

scholarly journals Segmental duplications are hot spots of copy number variants affecting barley gene content

2020 ◽  
Vol 103 (3) ◽  
pp. 1073-1088
Author(s):  
Gianluca Bretani ◽  
Laura Rossini ◽  
Chiara Ferrandi ◽  
Joanne Russell ◽  
Robbie Waugh ◽  
...  
Keyword(s):  
Hot Spots ◽  
Copy Number ◽  
Copy Number Variants ◽  
Gene Content ◽  
Segmental Duplications

Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants

2006 ◽  
Vol 38 (10) ◽  
pp. 1216-1220 ◽  
Author(s):  
Adnan Derti ◽  
Frederick P Roth ◽  
George M Church ◽  
C-ting Wu
Keyword(s):  
Copy Number ◽  
Copy Number Variants ◽  
Segmental Duplications ◽  
Ultraconserved Elements

scholarly journals Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome

2007 ◽  
Vol 104 (24) ◽  
pp. 10110-10115 ◽  
Author(s):  
J. O. Korbel ◽  
A. E. Urban ◽  
F. Grubert ◽  
J. Du ◽  
T. E. Royce ◽  
...  
Keyword(s):  
Human Genome ◽  
Copy Number ◽  
Copy Number Variants

scholarly journals Structural and copy number variants in the human genome: implications for psychiatry

2013 ◽  
Vol 202 (1) ◽  
pp. 5-6 ◽  
Author(s):  
David St Clair
Keyword(s):  
Brain Development ◽  
Human Genome ◽  
Copy Number ◽  
Copy Number Variants ◽  
Adult Brain ◽  
Normal Brain ◽  
Brain Functioning ◽  
Chromosomal Deletions ◽  
Normal Brain Development

SummaryCopy number variants are small chromosomal deletions and duplications. When they alter the dose of genes critical for normal brain development and adult brain functioning they may cause severe disorders such as autism and schizophrenia. Numerous such loci have recently been identified. They are offering amazing leads for neuropsychiatric research.

Mutational and selective effects on copy-number variants in the human genome

2007 ◽  
Vol 39 (S7) ◽  
pp. S22-S29 ◽  
Author(s):  
Gregory M Cooper ◽  
Deborah A Nickerson ◽  
Evan E Eichler
Keyword(s):  
Human Genome ◽  
Copy Number ◽  
Copy Number Variants ◽  
Selective Effects

scholarly journals Structural variation in the human genome: the impact of copy number variants on clinical diagnosis

2007 ◽  
Vol 9 (9) ◽  
pp. 600-606 ◽  
Author(s):  
Laia Rodriguez-Revenga ◽  
Montserrat Mila ◽  
Carla Rosenberg ◽  
Allen Lamb ◽  
Charles Lee
Keyword(s):  
Human Genome ◽  
Clinical Diagnosis ◽  
Copy Number ◽  
Structural Variation ◽  
Copy Number Variants ◽  
The Impact

The genomic architecture of segmental duplications and copy number variants in dogs

2009 ◽  
Vol 4 (2) ◽  
pp. 71-72
Author(s):  
Thomas J. Nicholas ◽  
Ze Cheng ◽  
Katrina L. Mealey ◽  
Evan E. Eichler ◽  
Joshua M. Akey
Keyword(s):  
Copy Number ◽  
Copy Number Variants ◽  
Segmental Duplications ◽  
Genomic Architecture

scholarly journals Segmental Duplications and Copy-Number Variation in the Human Genome

2005 ◽  
Vol 77 (1) ◽  
pp. 78-88 ◽  
Author(s):  
Andrew J. Sharp ◽  
Devin P. Locke ◽  
Sean D. McGrath ◽  
Ze Cheng ◽  
Jeffrey A. Bailey ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Human Genome ◽  
Copy Number ◽  
Segmental Duplications ◽  
Number Variation

scholarly journals Benchmarking challenging small variants with linked and long reads

2020 ◽  
Author(s):  
Justin Wagner ◽  
Nathan D Olson ◽  
Lindsay Harris ◽  
Ziad Khan ◽  
Jesse Farek ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Variants ◽  
Variant Calling ◽  
Segmental Duplications ◽  
False Negatives ◽  
Long Reads ◽  
New Variant ◽  
Long Read ◽  
Number Variation ◽  
Large Indels

AbstractGenome in a Bottle (GIAB) benchmarks have been widely used to help validate clinical sequencing pipelines and develop new variant calling and sequencing methods. Here we use accurate long and linked reads to expand the prior benchmark to include difficult-to-map regions and segmental duplications that are not readily accessible to short reads. Our new benchmark adds more than 300,000 SNVs, 50,000 indels, and 16 % new exonic variants, many in challenging, clinically relevant genes not previously covered (e.g., PMS2). We increase coverage of the autosomal GRCh38 assembly from 85 % to 92 %, while excluding problematic regions for benchmarking small variants (e.g., copy number variants and assembly errors) that should not have been in the previous version. Our new benchmark reliably identifies both false positives and false negatives across multiple short-, linked-, and long-read based variant calling methods. As an example of its utility, this benchmark identifies eight times more false negatives in a short read variant call set relative to our previous benchmark, mostly in difficult-to-map regions. To enable robust small variant benchmarking, we still exclude 3.6% of GRCh37 and 5.0% of GRCh38 in (1) highly repetitive regions such as large, highly similar segmental duplications and the centromere not accessible to our data and (2) regions where our sample is highly divergent from the reference due to large indels, structural variation, copy number variation, and/or errors in the reference (e.g., some KIR genes that have duplications in HG002). We have demonstrated the utility of this benchmark to assess performance in more challenging regions, which enables benchmarking in more difficult genes and continued technology and bioinformatics development. The v4.2.1 benchmarks are available under ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/.

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