Development of a simple SLA ‐1 copy‐number‐variation typing and the comparison of typing accuracy between real‐time quantitative and droplet digital PCR

2019 ◽  
Vol 50 (3) ◽  
pp. 315-316 ◽  
Author(s):  
Juyoung Lee ◽  
Minh Thong Le ◽  
Min‐Kyeung Choi ◽  
Van Chanh Quy Le ◽  
Hojun Choi ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Real Time ◽  
Copy Number ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Number Variation

scholarly journals Optimisation of droplet digital PCR for determining copy number variation of α-gliadin genes in mutant and gene-edited polyploid bread wheat

2020 ◽  
Vol 92 ◽  
pp. 102903 ◽  
Author(s):  
Aurélie Jouanin ◽  
Rubén Tenorio-Berrio ◽  
Jan G. Schaart ◽  
Fiona Leigh ◽  
Richard G.F. Visser ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Bread Wheat ◽  
Copy Number ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Number Variation

Analyzing Copy Number Variation with Droplet Digital PCR

2018 ◽  
pp. 143-160 ◽  
Author(s):  
Avery Davis Bell ◽  
Christina L. Usher ◽  
Steven A. McCarroll
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Number Variation

scholarly journals Killer-cell Immunoglobulin-like Receptor gene linkage and copy number variation analysis by droplet digital PCR

10.1186/gm537 ◽  
2014 ◽  
Vol 6 (3) ◽  
pp. 20 ◽  
Author(s):  
Chrissy h Roberts ◽  
Wei Jiang ◽  
Jyothi Jayaraman ◽  
John Trowsdale ◽  
Martin J Holland ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Receptor Gene ◽  
Killer Cell ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Variation Analysis ◽  
Gene Linkage ◽  
Copy Number Variation Analysis ◽  
Number Variation

scholarly journals Copy number variation of the putative speciation genes in the European house mouse hybrid zone

2021 ◽  
Author(s):  
Alexey Yanchukov ◽  
Zusana Hiadlovska ◽  
Zeljka Pezer ◽  
Milos Macholan ◽  
Jaroslav Pialek ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
House Mouse ◽  
Hybrid Zone ◽  
Copy Number ◽  
Digital Pcr ◽  
Gene Copy ◽  
Ancestral Population ◽  
Hybrid Zones ◽  
Interaction Sites ◽  
Number Variation

Hybrid zones have long been described as "windows on the evolutionary process", and studying them has become even more important since the advance in the genome analysis tools. The hybrid zone between two subspecies of the house mouse (Mus musculus musculus and Mus m. domesticus) is a unique model speciation system to study fine scale interactions of recently diverged genomes. Here, we explore the role of gene Copy Number Variation in shaping the barrier to introgression in the hybrid zone within a previously established transect in Central Europe. The CNV of seven pre-selected candidate genes was determined via droplet-digital PCR and analyzed in the context of ~500k SNPs, with the ancestral population (i.e. musculus or domesticus) of every SNP allele previously inferred in the admixed individuals (Baird et al., in prep.). The copy numbers of five genes were clearly associated with the prevalence of either musculus or domesticus genomes across the hybrid zone. In three cases, the highest and/or outlying levels of association were observed at or very close to the annotated positions of the respective gene amplicons, demonstrating the power of our approach in confirming the reference locations of copy number variants. Notably, several other reference locations were recognized as positive outliers in the association with particular CNV genes, possibly representing the extra gene copies and/or their epistatic interaction sites.

scholarly journals High levels of copy number variation of ampliconic genes across major human Y haplogroups

2017 ◽  
Author(s):  
Danling Ye ◽  
Arslan Zaidi ◽  
Marta Tomaszkiewicz ◽  
Corey Liebowitz ◽  
Michael DeGiorgio ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Y Chromosome ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Families ◽  
Digital Pcr ◽  
Gene Copy ◽  
Copy Numbers ◽  
Number Variation ◽  
Gene Copy Numbers

AbstractDue to its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100 males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared by males from very different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according to major Y haplogroups. Overall, only three gene families (DATZ, RBMY, TSPY) showed significant differences in copy number among major Y haplogroups, and the haplogroup of an individual could not be predicted based on his ampliconic gene copy numbers. Finally, we found a significant correlation between copy number variation and individual’s height (for three gene families), but not between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.

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