Bulk segregation analysis in NGS era: a review for its teenage years

Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.

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Segregation Analysis of HDL 3 -C Levels in Families of Patients Undergoing Coronary Arteriography at an Early Age

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/01.atv.15.9.1307 ◽

1995 ◽

Vol 15 (9) ◽

pp. 1307-1313 ◽

Cited By ~ 4

Author(s):

J. Coresh ◽

T.H. Beaty ◽

V.L. Prenger ◽

J. Xu ◽

P.O. Kwiterovich

Keyword(s):

Segregation Analysis ◽

Coronary Arteriography ◽

Early Age

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Paternal Uniparental Isodisomy of Chromosome 2 in a Patient with CNGA3-Associated Autosomal Recessive Achromatopsia

International Journal of Molecular Sciences ◽

10.3390/ijms22157842 ◽

2021 ◽

Vol 22 (15) ◽

pp. 7842

Author(s):

Susanne Kohl ◽

Britta Baumann ◽

Francesca Dassie ◽

Anja K. Mayer ◽

Maria Solaki ◽

...

Keyword(s):

Segregation Analysis ◽

Molecular Genetic ◽

Retinal Disease ◽

Underlying Mechanism ◽

Recurrence Risk ◽

Molecular Genetic Analysis ◽

Recessive Mutation ◽

Chromosome 2 ◽

Inherited Retinal Disease ◽

Uniparental Isodisomy

Achromatopsia (ACHM) is a rare autosomal recessively inherited retinal disease characterized by congenital photophobia, nystagmus, low visual acuity, and absence of color vision. ACHM is genetically heterogeneous and can be caused by biallelic mutations in the genes CNGA3, CNGB3, GNAT2, PDE6C, PDE6H, or ATF6. We undertook molecular genetic analysis in a single female patient with a clinical diagnosis of ACHM and identified the homozygous variant c.778G>C;p.(D260H) in the CNGA3 gene. While segregation analysis in the father, as expected, identified the CNGA3 variant in a heterozygous state, it could not be displayed in the mother. Microsatellite marker analysis provided evidence that the homozygosity of the CNGA3 variant is due to partial or complete paternal uniparental isodisomy (UPD) of chromosome 2 in the patient. Apart from the ACHM phenotype, the patient was clinically unsuspicious and healthy. This is one of few examples proving UPD as the underlying mechanism for the clinical manifestation of a recessive mutation in a patient with inherited retinal disease. It also highlights the importance of segregation analysis in both parents of a given patient or especially in cases of homozygous recessive mutations, as UPD has significant implications for genetic counseling with a very low recurrence risk assessment in such families.

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Hereditary polyneuropathy in the Alaskan Malamute

Tierärztliche Praxis Ausgabe K Kleintiere / Heimtiere ◽

10.1055/s-0038-1623617 ◽

2012 ◽

Vol 40 (01) ◽

pp. 26-34 ◽

Cited By ~ 3

Author(s):

T. Bilzer ◽

S. Petri ◽

G. Schanen ◽

M. Fehr ◽

O. Distl ◽

...

Keyword(s):

Segregation Analysis ◽

Nerve Conduction Velocity ◽

Axonal Degeneration ◽

Phenotypic Expression ◽

Disease Status ◽

Nerve Biopsy ◽

Hereditary Disease ◽

Genetic Transmission ◽

Clinically Normal ◽

Background Material

Summary Objective: To prove the hypothesis that a polyneuropathy in Alaskan Malamutes has a genetic background. Material and methods: Pedigrees of 131 related Alaskan Malamutes were included in the current study. Neurological examination, electrodiagnosis as well as muscle and nerve biopsies could be performed in 10 dogs. Information about the disease status of the other 121 Alaskan Malamutes were supplied by referring veterinarians, breeders and owners. Segregation analysis using four different models (monogenic, polygenic, mixed monogenicpolygenic and the phenotypic model) was performed on 71 dogs to test the different mechanisms of genetic transmission. Results: In seven clinically affected dogs abnormal electromyographic findings and reduced nerve conduction velocity were detected. Suspected diagnosis of polyneuropathy was confirmed by nerve biopsy results, characterized by axonal degeneration and hypomyelination. Muscle specimens revealed signs of neurogenic myopathy. Three related clinically normal Alaskan Malamutes also displayed moderate neuromuscular changes in histopathology. In the segregation analysis the polygenic model proved as best suitable to explain the observed segregation pattern among all other models tested. Conclusion: The current study could demonstrate that polyneuropathy in Alaskan Malamutes is a hereditary disease with variable phenotypic expression ranging from severely affected to subclinical forms, which has to be considered in future gene analysis studies.

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