scholarly journals Genome‐Wide Fitness and Genetic Interactions Determined by Tn‐seq, a High‐Throughput Massively Parallel Sequencing Method for Microorganisms

2010 ◽  
Vol 19 (1) ◽  
Author(s):  
Tim van Opijnen ◽  
Andrew Camilli
Keyword(s):  
High Throughput ◽  
Massively Parallel Sequencing ◽  
Genetic Interactions ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Genome Wide ◽  
Sequencing Method

scholarly journals Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

2021 ◽  
Author(s):  
Stella C. Yuan ◽  
Eric Malekos ◽  
Melissa T. R. Hawkins
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Museum Specimens ◽  
Museum Specimen ◽  
Genotyping Errors ◽  
Allelic Dropout ◽  
Parallel Sequencing ◽  
Sequencing Technologies

AbstractThe use of museum specimens held in natural history repositories for population and conservation genetic research is increasing in tandem with the use of massively parallel sequencing technologies. Short Tandem Repeats (STRs), or microsatellite loci, are commonly used genetic markers in wildlife and population genetic studies. However, they traditionally suffered from a host of issues including length homoplasy, high costs, low throughput, and difficulties in reproducibility across laboratories. Massively parallel sequencing technologies can address these problems, but the incorporation of museum specimen derived DNA suffers from significant fragmentation and exogenous DNA contamination. Combatting these issues requires extra measures of stringency in the lab and during data analysis, yet there have not been any high-throughput sequencing studies evaluating microsatellite allelic dropout from museum specimen extracted DNA. In this study, we evaluate genotyping errors derived from mammalian museum skin DNA extracts for previously characterized microsatellites across PCR replicates utilizing high-throughput sequencing. We found it useful to classify samples based on DNA concentration, which determined the rate by which genotypes were accurately recovered. Longer microsatellites performed worse in all museum specimens. Allelic dropout rates across loci were dependent on sample quantity, with high concentration museum specimens performing as well and recovering quality metrics nearly as high as the frozen tissue sample. Based on our results, we provide a set of best practices for quality assurance and incorporation of reliable genotypes from museum specimens.

scholarly journals High throughput whole mitochondrial genome sequencing by two platforms of massively parallel sequencing

BMC Genomics ◽  
2014 ◽  
Vol 15 (Suppl 2) ◽  
pp. P7 ◽  
Author(s):  
Seung Seo ◽  
Xiangpei Zeng ◽  
Mourad Assidi ◽  
Bobby LaRue ◽  
Jonathan King ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequencing ◽  
High Throughput ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Parallel Sequencing

Abstract LB-122: High-throughput tumor genomic profiling by massively parallel sequencing

2010 ◽  
Author(s):  
Nikhil Wagle ◽  
Matt Davis ◽  
Michael F. Berger ◽  
Brendan Blumenstiel ◽  
Matthew Defelice ◽  
...  
Keyword(s):  
High Throughput ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Genomic Profiling ◽  
Parallel Sequencing

Comprehensive preimplantation genetic testing by massively parallel sequencing

2020 ◽  
Author(s):  
Songchang Chen ◽  
Xuyang Yin ◽  
Sijia Zhang ◽  
Jun Xia ◽  
Ping Liu ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Genome Sequencing ◽  
Massively Parallel Sequencing ◽  
Science And Technology ◽  
Family Members ◽  
Snp Array ◽  
Massively Parallel ◽  
Preimplantation Genetic Testing ◽  
Parallel Sequencing ◽  
Genome Wide

Abstract STUDY QUESTION Can whole genome sequencing (WGS) offer a relatively cost-effective approach for embryonic genome-wide haplotyping and preimplantation genetic testing (PGT) for monogenic disorders (PGT-M), aneuploidy (PGT-A) and structural rearrangements (PGT-SR)? SUMMARY ANSWER Reliable genome-wide haplotyping, PGT-M, PGT-A and PGT-SR could be performed by WGS with 10× depth of parental and 4× depth of embryonic sequencing data. WHAT IS KNOWN ALREADY Reduced representation genome sequencing with a genome-wide next-generation sequencing haplarithmisis-based solution has been verified as a generic approach for automated haplotyping and comprehensive PGT. Several low-depth massively parallel sequencing (MPS)-based methods for haplotyping and comprehensive PGT have been developed. However, an additional family member, such as a sibling, or a proband, is required for PGT-M haplotyping using low-depth MPS methods. STUDY DESIGN, SIZE, DURATION In this study, 10 families that had undergone traditional IVF-PGT and 53 embryos, including 13 embryos from two PGT-SR families and 40 embryos from eight PGT-M families, were included to evaluate a WGS-based method. There were 24 blastomeres and 29 blastocysts in total. All embryos were used for PGT-A. Karyomapping validated the WGS results. Clinical outcomes of the 10 families were evaluated. PARTICIPANTS/MATERIALS, SETTING, METHODS A blastomere or a few trophectoderm cells from the blastocyst were biopsied, and multiple displacement amplification (MDA) was performed. MDA DNA and bulk DNA of family members were used for library construction. Libraries were sequenced, and data analysis, including haplotype inheritance deduction for PGT-M and PGT-SR and read-count analysis for PGT-A, was performed using an in-house pipeline. Haplotyping with a proband and parent-only haplotyping without additional family members were performed to assess the WGS methodology. Concordance analysis between the WGS results and traditional PGT methods was performed. MAIN RESULTS AND THE ROLE OF CHANCE For the 40 PGT-M and 53 PGT-A embryos, 100% concordance between the WGS and single-nucleotide polymorphism (SNP)-array results was observed, regardless of whether additional family members or a proband was included for PGT-M haplotyping. For the 13 embryos from the two PGT-SR families, the embryonic balanced translocation was detected and 100% concordance between WGS and MicroSeq with PCR-seq was demonstrated. LIMITATIONS, REASONS FOR CAUTION The number of samples in this study was limited. In some cases, the reference embryo for PGT-M or PGT-SR parent-only haplotyping was not available owing to failed direct genotyping. WIDER IMPLICATIONS OF THE FINDINGS WGS-based PGT-A, PGT-M and PGT-SR offered a comprehensive PGT approach for haplotyping without the requirement for additional family members. It provided an improved complementary method to PGT methodologies, such as low-depth MPS- and SNP array-based methods. STUDY FUNDING/COMPETING INTEREST(S) This research was supported by the research grant from the National Key R&D Program of China (2018YFC0910201 and 2018YFC1004900), the Guangdong province science and technology project of China (2019B020226001), the Shenzhen Birth Defect Screening Project Lab (JZF No. [2016] 750) and the Shenzhen Municipal Government of China (JCYJ20170412152854656). This work was also supported by the National Natural Science Foundation of China (81771638, 81901495 and 81971344), the National Key R&D Program of China (2018YFC1004901 and 2016YFC0905103), the Shanghai Sailing Program (18YF1424800), the Shanghai Municipal Commission of Science and Technology Program (15411964000) and the Shanghai ‘Rising Stars of Medical Talent’ Youth Development Program Clinical Laboratory Practitioners Program (201972). The authors declare no competing interests. TRIAL REGISTRATION NUMBER N/A.

High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq

2014 ◽  
Vol 12 ◽  
pp. 128-135 ◽  
Author(s):  
Jonathan L. King ◽  
Bobby L. LaRue ◽  
Nicole M. Novroski ◽  
Monika Stoljarova ◽  
Seung Bum Seo ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
High Throughput ◽  
Massively Parallel Sequencing ◽  
Illumina Miseq ◽  
Massively Parallel ◽  
High Quality ◽  
Parallel Sequencing ◽  
Human Mitochondrial Genome

scholarly journals Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

2010 ◽  
Vol 4 (1-4) ◽  
pp. 35-48 ◽  
Author(s):  
Kousuke Tanimoto ◽  
Katsuya Tsuchihara ◽  
Akinori Kanai ◽  
Takako Arauchi ◽  
Hiroyasu Esumi ◽  
...  
Keyword(s):  
Cell Lines ◽  
Binding Sites ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Genome Wide

scholarly journals High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing

2011 ◽  
Vol 2 (1) ◽  
pp. 82-93 ◽  
Author(s):  
Nikhil Wagle ◽  
Michael F. Berger ◽  
Matthew J. Davis ◽  
Brendan Blumenstiel ◽  
Matthew DeFelice ◽  
...  
Keyword(s):  
High Throughput ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Genomic Alterations ◽  
Parallel Sequencing ◽  
High Throughput Detection
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