Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua

2013 ◽  
Vol 82 (3) ◽  
pp. 944-958 ◽  
Author(s):  
J. Carlsson ◽  
D. T. Gauthier ◽  
J. E. L. Carlsson ◽  
J. P. Coughlan ◽  
E. Dillane ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
De Novo Assembly ◽  
Gadus Morhua ◽  
De Novo ◽  
Atlantic Cod ◽  
Model Organism ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Reduced Representation

scholarly journals Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e88998 ◽  
Author(s):  
Ron Ophir ◽  
Amir Sherman ◽  
Mor Rubinstein ◽  
Ravit Eshed ◽  
Michal Sharabi Schwager ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
De Novo Assembly ◽  
De Novo ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Development and characterisation of microsatellite and single nucleotide polymorphism markers in Atlantic cod (Gadus morhua L.)

Aquaculture ◽  
2007 ◽  
Vol 272 ◽  
pp. S250 ◽  
Author(s):  
M. Delghandi ◽  
J. Stenvik ◽  
T. Moen ◽  
M.S. Wesmajervi ◽  
J.I. Westgård ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Development of single nucleotide polymorphism markers for Atlantic cod (Gadus morhua) using expressed sequences

Aquaculture ◽  
2009 ◽  
Vol 296 (1-2) ◽  
pp. 7-14 ◽  
Author(s):  
Sophie Hubert ◽  
Jillian Tarrant Bussey ◽  
Brent Higgins ◽  
Bruce A. Curtis ◽  
Sharen Bowman
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Prenatal Diagnosis of 17p11.2 Copy Number Abnormalities Associated With Smith–Magenis and Potocki–Lupski Syndromes in Fetuses

2021 ◽  
Vol 12 ◽  
Author(s):  
Meiying Cai ◽  
Xianguo Fu ◽  
Liangpu Xu ◽  
Na Lin ◽  
Hailong Huang
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Prenatal Diagnosis ◽  
Copy Number ◽  
De Novo ◽  
Single Nucleotide Polymorphism Array ◽  
Copy Number Variant ◽  
Prenatal Ultrasound ◽  
Nucleotide Polymorphism ◽  
Array Analysis ◽  
Single Nucleotide

Smith-Magenis syndrome and Potocki-Lupski syndrome are rare autosomal dominant diseases. Although clinical phenotypes of adults and children have been reported, fetal ultrasonic phenotypes are rarely reported. A retrospective analysis of 6,200 pregnant women who received invasive prenatal diagnosis at Fujian Provincial Maternal and Child Health Hospital between October 2016 and January 2021 was performed. Amniotic fluid or umbilical cord blood was extracted for karyotyping and single nucleotide polymorphism array analysis. Single nucleotide polymorphism array analysis revealed six fetuses with copy number variant changes in the 17p11.2 region. Among them, one had a copy number variant microdeletion in the 17p11.2 region, which was pathogenically analyzed and diagnosed as Smith-Magenis syndrome. Five fetuses had copy number variant microduplications in the 17p11.2 region, which were pathogenically analyzed and diagnosed as Potocki-Lupski syndrome. The prenatal ultrasound phenotypes of the six fetuses were varied. The parents of two fetuses with Potocki-Lupski syndrome refused verification. Smith-Magenis syndrome in one fetus and Potocki-Lupski in another were confirmed as de novo. Potocki-Lupski syndrome in two fetuses was confirmed to be from maternal inheritance. The prenatal ultrasound phenotypes of Smith-Magenis syndrome and Potocki-Lupski syndrome in fetuses vary; single nucleotide polymorphism array analysis is a powerful diagnostic tool for these diseases. The ultrasonic phenotypes of these cases may enrich the clinical database.

Dissecting Clonal Diversity in Complex Leukemia Samples with Next Generation Single Nucleotide Polymorphism (SNP)-Copy Number Arrays,

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3550-3550
Author(s):  
Sanidad A Marc ◽  
Marilyn L Slovak ◽  
Philip N Mowry ◽  
Joey C Kelly ◽  
Daniel M Jones
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Copy Number ◽  
Dna Microarrays ◽  
De Novo ◽  
Clonal Diversity ◽  
Genetic Alterations ◽  
Next Generation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Oligonucleotide Arrays

Abstract Abstract 3550 Introduction: The genetic loci altered in many de novo leukemia cases are relatively well-understood and can be accurately assessed by current cytogenetic techniques including multi-probe fluorescence in situ hybridization (FISH). However, identifying the cancer genes involved in complex leukemia karyotypes remains problematic due to the presence of multiple secondary structural rearrangements observed in subclonal populations. These alterations often affect both chromosome (chr) homologues and predominantly involve chr 1, 3, 5, 7, 12 and 17. Such clonal diversity within a tumor reflects the underlying biologically-selected sequential and multiple rearrangements and can, if carefully mapped, highlight the locations of tumor suppressor genes and modifiers involved in disease progression. Previous generations of DNA microarrays have proven useful in dissecting genomic changes in the predominant tumor clone, including copy-neutral loss of heterozygosity (CN-LOH) when single nucleotide polymorphism (SNP) arrays are used. However, a well-known shortcoming of DNA microarrays to date has been their limited sensitivity for accurately detecting low level mosaicism (<20%) and subclonal changes that are common in complex karyotypes. Methods: Using leukemia cases that showed complex karyotypes with up to 4 subclones, we compared the ability of standard (SNP 6.0, Affymetrix) and next-generation (Cytoscan HD, Affymetrix) SNP/copy number oligonucleotide arrays to accurately detect the observed karyotypic subclones and more precisely delineate areas of complex chromosomal alterations. Genomic DNA extracted from fresh material or 24∼48 hour short-term cultures from 8 patients with either de novo or previously treated chronic lymphocytic leukemia (CLL) was assessed on the SNP 6.0 and Cytoscan HD platforms and then compared with their karyotype, and/or supporting FISH studies. Copy number alterations and CN-LOH calls were made using ChAS software (Affymetrix), with the degree of clonal mosaicism analyzed for segmental increments of each chromosome by averaging the smooth signal data. Results and Conclusion: For all 53 CN-LOH and copy number calls, the two arrays gave identical detection rates and similar alteration boundaries in 34 instances (64.1% concordance). The genetic alterations that differed among the cytogenetically-related clones (subclones) were subclonal, in all but 3 instances, and most frequently involved chr 1 and 5. In general, the Cytoscan HD arrays were able to accurately detect karyotypically-confirmed subclones down to the 20% level (as well as distinguishing 90% vs. 100% calls), as opposed to the 30–50% level seen with the SNP 6.0 arrays. Improved detection of the discrete subclones or lower level clonality was attributed to more precise allele peak heights that did not require smoothing. Next-generation SNP/copy number oligonucleotide arrays show great promise in providing additive value to leukemic genomic profiling by clear visual separation of multiple genomic alterations within clonally diverse samples with the potential of identifying novel genetic alterations that may be important in disease progression. Disclosures: No relevant conflicts of interest to declare.

Sign in / Sign up

Export Citation Format

Share Document