Structural variants of the α-fetoprotein gene in different inbred strains of rat

1984 ◽  
Vol 195 (1-2) ◽  
pp. 153-158 ◽  
Author(s):  
Andras Gal ◽  
Jean-Louis Nahon ◽  
Gérard Lucotte ◽  
José M. Sala-Trepat
Keyword(s):  
Inbred Strains ◽  
Structural Variants

scholarly journals SVJAM: Joint Analysis of Structural Variants Using Linked Read Sequencing Data

2021 ◽  
Author(s):  
Mustafa Hakan Gunturkun ◽  
Flavia Villani ◽  
Vincenza Colonna ◽  
David Ashbrook ◽  
Robert W Williams ◽  
...  
Keyword(s):  
Distance Measure ◽  
Dimensional Space ◽  
Principal Component ◽  
Inbred Strains ◽  
Joint Analysis ◽  
Structural Variants ◽  
Sequencing Data ◽  
High Molecular Weight Dna ◽  
Sample Distribution ◽  
Overlapping Data

Linked-read whole genome sequencing methods, such as the 10x Chromium, attach a unique molecular barcode to each high molecular weight DNA molecule. The samples are then sequenced using short-read technology. During analysis, sequence reads sharing the same barcode are aligned to adjacent genomic locations. The pattern of barcode sharing between genomic regions allows the discovery of large structural variants (SVs) in the range of 1 Kb to a few Mb. Most SV calling methods for these data, such as LongRanger, analyze one sample at a time and often produces inconsistent results for the same genomic location across multiple samples. We developed a method, SVJAM, for joint calling of SVs, using data from 152 members of the BXD family of recombinant inbred strains of mice. Our method first collects candidate SV regions from single sample analysis, such as those produced by LongRanger. We then retrieve barcode overlapping data from all samples for each region. These data are organized as a high dimensional matrix. The dimension of this matrix is then reduced using principal component analysis. Samples projected onto a two dimensional space formed by the first two principal components forms two or three clusters based on their genotype, representing the reference, alternative, or heterozygotic alleles. We developed a novel distance measure for hierarchical clustering and rotating the axes to find the optimal clustering results. We also developed an algorithm to decide whether the pattern of sample distribution is best fitted with one, two, or three genotypes. For each sample, we calculate its membership score for each genotype. We compared results produced by SVJAM with LongRanger and few methods that rely on PacBio or Oxford Nanopore data. In a comparison of SVJAM with SV detected using long-read sequencing data for the DBA/2J strain, we found that our results recovered many SVs missed by LongRanger. We also found many SVs called by LongRanger were assigned with an incorrect SV type. Our algorithm also consistently identified heterozygotic regions.

Genome-Wide Analysis of Polygenic Cardiac Traits in Medaka Inbred Strains

2020 ◽  
Author(s):  
J. Gierten ◽  
T. Fitzgerald ◽  
F. Loosli ◽  
M. Gorenflo ◽  
E. Birney ◽  
...  
Keyword(s):  
Inbred Strains ◽  
Genome Wide Analysis ◽  
Genome Wide

Effects of Foster Nursing on Alcohol Selection in Inbred Strains of Mice

1972 ◽  
Vol 33 (2) ◽  
pp. 494-503 ◽  
Author(s):  
Setsuo Komura ◽  
Masao Ueda ◽  
Toshikiyo Kobayashi
Keyword(s):  
Inbred Strains ◽  
Inbred Strains Of Mice

Studies on Inbred Strains of Drosophila melanogaster

1965 ◽  
Vol 99 (909) ◽  
pp. 495-510 ◽  
Author(s):  
Bruce Wallace ◽  
Carol Madden
Keyword(s):  
Drosophila Melanogaster ◽  
Inbred Strains

Duplications and deletions of Vh genes in inbred strains of mice

1988 ◽  
Vol 28 (2) ◽  
pp. 125-135 ◽  
Author(s):  
Adele Tutte ◽  
Roy Riblet
Keyword(s):  
Inbred Strains ◽  
Inbred Strains Of Mice ◽  
Vh Genes

scholarly journals Genetic Control of Mammalian Meiotic Recombination. I. Variation in Exchange Frequencies Among Males From Inbred Mouse Strains

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 297-306 ◽  
Author(s):  
Kara E Koehler ◽  
Jonathan P Cherry ◽  
Audrey Lynn ◽  
Patricia A Hunt ◽  
Terry J Hassold
Keyword(s):  
Meiotic Recombination ◽  
Inbred Mouse ◽  
Inbred Strains ◽  
Male Meiosis ◽  
Mouse Strains ◽  
Recombination Rates ◽  
The Mean ◽  
Genetic Background Effects ◽  
Exchange Patterns ◽  
Positive Interference

AbstractGenetic background effects on the frequency of meiotic recombination have long been suspected in mice but never demonstrated in a systematic manner, especially in inbred strains. We used a recently described immunostaining technique to assess meiotic exchange patterns in male mice. We found that among four different inbred strains—CAST/Ei, A/J, C57BL/6, and SPRET/Ei—the mean number of meiotic exchanges per cell and, thus, the recombination rates in these genetic backgrounds were significantly different. These frequencies ranged from a low of 21.5 exchanges in CAST/Ei to a high of 24.9 in SPRET/Ei. We also found that, as expected, these crossover events were nonrandomly distributed and displayed positive interference. However, we found no evidence for significant differences in the patterns of crossover positioning between strains with different exchange frequencies. From our observations of >10,000 autosomal synaptonemal complexes, we conclude that achiasmate bivalents arise in the male mouse at a frequency of 0.1%. Thus, special mechanisms that segregate achiasmate chromosomes are unlikely to be an important component of mammalian male meiosis.

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