NCBI at ASHG 2019: Two Data CoLabs Demonstrate How to Analyze NextGen Sequence Data and Access Genetic Variation Population Data


NCBI will be attending the American Society of Human Genetics (ASHG) 2019 in Houston Texas on Oct 15-19.

This year, we will be presenting two CoLabs – interactive sessions where you can learn about new NCBI tools and resources. Read on below for a description of each CoLab and join us at ASHG next week!

“NCBI resources for NextGen sequence analysis”

  • Date and Time: Wednesday, October 16, 2018 at 4:00PM
  • Location: CoLab Theater 3, Booth 1209
  • Audience: Genomics and genetics researchers

Learn about a suite of NCBI resources that support multiple aspects of nextgen sequence analyses, including quality control, alignment, data visualization, and results interpretation. In this workshop, we’ll demonstrate how to access and apply these resources for both SRA and user-supplied RNASeq/DNASeq datasets. Whether you’re embarking on your first analysis or already have a background in bioinformatics, you’ll find tools that meet your needs. Topics will include the following:

  • Aligning your own or SRA read data to the reference or other genome assemblies with Magic-BLAST
  • Visualizing nextgen read alignments in NCBI’s Genome Data Viewer with specific tracks and annotations for variant identification, finding allele frequency information, and evaluating variant significance (functional and clinical)
  • Accessing newly developed cloud-based BLAST resources

Everyone attending this CoLab will receive a handout with illustrated steps to reproduce the demonstrated examples.

“Using dbGaP aggregated allele frequency and other large data sets in dbSNP to improve human genetic variation interpretation”

  • Date and Time: Friday, October 18, 2018 at 10:00AM
  • Location: CoLab Theater 1, Booth 345
  • Audience: Genomics and genetics researchers

Population variation frequency information can help assess the potential impact of human genetic variants. We have included relevant population frequency information on NCBI dbSNP records from research projects such as 1000 Genomes, ExAC, GnomAD, TopMed, and from other submissions. A new initiative at NCBI takes advantage of the wealth of clinical study data in the dbGaP database to create the dbGaP Aggregated Dataset. Based on more than 150,000 subjects in 60 dbGaP studies, the initial public release of this dataset provides population allele frequencies for more than 500 million known genetic variations and more than 20 million novel variations. We have added these new population frequency data to our dbSNP and ClinVar records, and you can acces these data both from our FTP site for bulk download and through the SPDI APIs. This CoLab presentation will introduce available population variation datasets at NCBI, show you how to find the data, and demonstrate how they can be used to interpret and prioritize variants for clinical and research.

To stay up-to-date about NCBI staff activities at ASHG 2019, follow us on Twitter at @NCBI and for more information about other NCBI presentations at ASHG, check the NCBI Conferences and Presentations page.

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