A Proposed Clinical Decision Support Architecture Capable of Supporting Whole Genome Sequence Information

AbstractIn this paper we extend multi-locus iterative peeling to be a computationally efficient method for calling, phasing, and imputing sequence data of any coverage in small or large pedigrees. Our method, called hybrid peeling, uses multi-locus iterative peeling to estimate shared chromosome segments between parents and their offspring, and then uses single-locus iterative peeling to aggregate genomic information across multiple generations. Using a synthetic dataset, we first analysed the performance of hybrid peeling for calling and phasing alleles in disconnected families, families which contained only a focal individual and its parents and grandparents. Second, we analysed the performance of hybrid peeling for calling and phasing alleles in the context of the full pedigree. Third, we analysed the performance of hybrid peeling for imputing whole genome sequence data to the remaining individuals in the population. We found that hybrid peeling substantially increase the number of genotypes that were called and phased by leveraging sequence information on related individuals. The calling rate and accuracy increased when the full pedigree was used compared to a reduced pedigree of just parents and grandparents. Finally, hybrid peeling accurately imputed whole genome sequence information to non-sequenced individuals. We believe that this algorithm will enable the generation of low cost and high accuracy whole genome sequence data in many pedigreed populations. We are making this algorithm available as a standalone program called AlphaPeel.

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The Need for Clinical Decision Support Integrated with the Electronic Health Record for the Clinical Application of Whole Genome Sequencing Information

Journal of Personalized Medicine ◽

10.3390/jpm3040306 ◽

2013 ◽

Vol 3 (4) ◽

pp. 306-325 ◽

Cited By ~ 14

Author(s):

Brandon Welch ◽

Kensaku Kawamoto

Keyword(s):

Decision Support ◽

Electronic Health Record ◽

Whole Genome Sequencing ◽

Clinical Application ◽

Genome Sequencing ◽

Clinical Decision Support ◽

Clinical Decision ◽

Health Record ◽

Whole Genome ◽

Electronic Health

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A genome-wide resource of intron spanning primers compatible for quantitative PCR and intron length polymorphism in rice

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.79.2.15 ◽

2019 ◽

Vol 79 (02) ◽

Author(s):

Humira Sonah ◽

Hasthi Ram ◽

Bikram Pratap Singh ◽

Jawaharlal Katara ◽

Radha Chopra ◽

...

Keyword(s):

Quantitative Pcr ◽

Genome Sequence ◽

Sequence Variation ◽

Whole Genome Sequence ◽

Pcr Analysis ◽

Sequence Information ◽

Whole Genome ◽

Intron Length Polymorphism ◽

Genome Wide ◽

A Genome

Whole genome sequence availability in rice has provided several advantages for genomics as well as other omics assisted applications. Genome-wide molecular markers are one of such availability that has exceptional importance in modern plant breeding. In the present study, a resource of intron-spanning primers (ISPs) was developed using whole genome sequence information of two rice subspecies, japonica (cv. Nipponbare) and indica (cv. 93-11). The ISPs were designed in a way that the PCR using a cDNA template will yield 60 to 100 base pair size amplicon ideal for the quantitative PCR analysis. Whereas, PCR using genomic DNA will amplify the introns, which are more prone to sequence variation. The sequence variation in the intron serves as an excellent marker resource. The application of ISPs was demonstrated by characterizing 12 diverse rice cultivars. A total of eight out of ten ISPs were found to be polymorphic. The resource will be helpful for the rice molecular biologist and breeder community.

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Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense

10.1101/2021.06.17.448907 ◽

2021 ◽

Author(s):

Kenta Shirasawa ◽

Nobuo Kobayashi ◽

Akira Nakatsuka ◽

Hideya Ohta ◽

Sachiko Isobe

Keyword(s):

Genome Sequence ◽

Single Molecule ◽

Sequence Information ◽

Whole Genome ◽

Closely Related Species ◽

Chiba Prefecture ◽

Genome Sequence Assembly ◽

Genome Sequence Information ◽

Relationship Of ◽

Long Fragment Read

To enhance the genomics and genetics of azalea, the whole-genome sequences of two species of Rhododendron were determined and analyzed in this study: Rhododendron ripense, the cytoplasmic donor and ancestral species of large-flowered and evergreen azalea cultivars, respectively; and Rhododendron kiyosumense, a native of Chiba prefecture (Japan) seldomly bred and cultivated. A chromosome-level genome sequence assembly of R. ripense was constructed by single-molecule real-time (SMRT) sequencing and genetic mapping, while the genome sequence of R. kiyosumense was assembled using the single-tube long fragment read (stLFR) sequencing technology. The R. ripense genome assembly contained 319 contigs (506.7 Mb; N50 length: 2.5 Mb) and was assigned to the genetic map to establish 13 pseudomolecule sequences. On the other hand, the genome of R. kiyosumense was assembled into 32,308 contigs (601.9 Mb; N50 length: 245.7 kb). A total of 34,606 genes were predicted in the R. ripense genome, while 35,785 flower and 48,041 leaf transcript isoforms were identified in R. kiyosumense through Iso-Seq analysis. Overall, the genome sequence information generated in this study enhances our understanding of genome evolution in the Ericales and reveals the phylogenetic relationship of closely-related species. This information will also facilitate the development of phenotypically attractive azalea cultivars.

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