scholarly journals Evaluation of the genetic basis of primary hypoadrenocorticism in Standard Poodles using SNP array genotyping and whole-genome sequencing

2016 ◽  
Vol 28 (1-2) ◽  
pp. 56-65 ◽  
Author(s):  
Steven G. Friedenberg ◽  
Katharine F. Lunn ◽  
Kathryn M. Meurs
2021 ◽  
Vol 5 (Supplement_S1) ◽  
pp. S1-S5
Author(s):  
Alexa M Barber ◽  
Alyssa Helms ◽  
Riley Thompson ◽  
Brian K Whitlock ◽  
David J Steffen ◽  
...  

2013 ◽  
Vol 93 (3) ◽  
pp. 452-462 ◽  
Author(s):  
Dan Zhou ◽  
Nitin Udpa ◽  
Roy Ronen ◽  
Tsering Stobdan ◽  
Junbin Liang ◽  
...  

Neurogenetics ◽  
2016 ◽  
Vol 17 (4) ◽  
pp. 265-270 ◽  
Author(s):  
Kishore R Kumar ◽  
G.M. Wali ◽  
Mahesh Kamate ◽  
Gautam Wali ◽  
André E Minoche ◽  
...  

2012 ◽  
Vol 18 (16) ◽  
pp. 4257-4265 ◽  
Author(s):  
Christine A. Iacobuzio-Donahue ◽  
Victor E. Velculescu ◽  
Christopher L. Wolfgang ◽  
Ralph H. Hruban

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Ho Jang ◽  
Youngmi Hur ◽  
Hyunju Lee

Abstract DNA copy number alterations (CNAs) are the main genomic events that occur during the initiation and development of cancer. Distinguishing driver aberrant regions from passenger regions, which might contain candidate target genes for cancer therapies, is an important issue. Several methods for identifying cancer-driver genes from multiple cancer patients have been developed for single nucleotide polymorphism (SNP) arrays. However, for NGS data, methods for the SNP array cannot be directly applied because of different characteristics of NGS such as higher resolutions of data without predefined probes and incorrectly mapped reads to reference genomes. In this study, we developed a wavelet-based method for identification of focal genomic alterations for sequencing data (WIFA-Seq). We applied WIFA-Seq to whole genome sequencing data from glioblastoma multiforme, ovarian serous cystadenocarcinoma and lung adenocarcinoma, and identified focal genomic alterations, which contain candidate cancer-related genes as well as previously known cancer-driver genes.


2014 ◽  
Vol 21 ◽  
pp. 54-57 ◽  
Author(s):  
Vartul Sangal ◽  
Andreas Burkovski ◽  
Alison C. Hunt ◽  
Becky Edwards ◽  
Jochen Blom ◽  
...  

2020 ◽  
Author(s):  
James R Mickelson ◽  
Katie M Minor ◽  
Ling T Guo ◽  
Steven G Friedenberg ◽  
Jonah N Cullen ◽  
...  

Abstract BackgroundA cohort of related miniature dachshund dogs with exercise intolerance, stiff gait, dysphagia, myoglobinuria and markedly elevated serum creatine kinase activities were identified. MethodsMuscle biopsy histopathology, immunofluorescence microscopy, and western blotting, were combined to identify the specific pathologic phenotype of the myopathy, and whole genome SNP array genotype data and whole genome sequencing were combined to determine its genetic basis.ResultsMuscle biopsies were dystrophic. Sarcoglycanopathy, a form of limb-girdle muscular dystrophy, was suspected based on immunostaining and western blotting, where α, β, and γ-sarcoglycan were all absent or reduced. Genetic mapping and whole genome sequencing identified a premature stop codon mutation in the sarcoglycan A subunit gene ( SGCA ). Affected dachshunds were confirmed on several continents. ConclusionsThis first SGCA mutation found in dogs adds to the literature of genetic bases of canine muscular dystrophies and their usefulness as comparative models of human disease.


Cancers ◽  
2021 ◽  
Vol 13 (24) ◽  
pp. 6283
Author(s):  
Migle Gabrielaite ◽  
Mathias Husted Torp ◽  
Malthe Sebro Rasmussen ◽  
Sergio Andreu-Sánchez ◽  
Filipe Garrett Vieira ◽  
...  

Copy-number variations (CNVs) have important clinical implications for several diseases and cancers. Relevant CNVs are hard to detect because common structural variations define large parts of the human genome. CNV calling from short-read sequencing would allow single protocol full genomic profiling. We reviewed 50 popular CNV calling tools and included 11 tools for benchmarking in a reference cohort encompassing 39 whole genome sequencing (WGS) samples paired current clinical standard—SNP-array based CNV calling. Additionally, for nine samples we also performed whole exome sequencing (WES), to address the effect of sequencing protocol on CNV calling. Furthermore, we included Gold Standard reference sample NA12878, and tested 12 samples with CNVs confirmed by multiplex ligation-dependent probe amplification (MLPA). Tool performance varied greatly in the number of called CNVs and bias for CNV lengths. Some tools had near-perfect recall of CNVs from arrays for some samples, but poor precision. Several tools had better performance for NA12878, which could be a result of overfitting. We suggest combining the best tools also based on different methodologies: GATK gCNV, Lumpy, DELLY, and cn.MOPS. Reducing the total number of called variants could potentially be assisted by the use of background panels for filtering of frequently called variants.


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