How biorepositories can help your research
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How Biorepositories Can Help Your Research. Tatiana Foroud, Ph.D. Department of Medical and Molecular Genetics. Overview. Sample collection for genetic studies Typical DNA applications for genetic studies Results from several ongoing studies. Collecting Samples for Genetic Studies.

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How biorepositories can help your research

How Biorepositories Can Help Your Research

Tatiana Foroud, Ph.D.

Department of Medical

and Molecular Genetics


Overview

Overview

  • Sample collection for genetic studies

  • Typical DNA applications for genetic studies

  • Results from several ongoing studies


Collecting samples for genetic studies

Collecting Samples for Genetic Studies

  • Often the overlooked item in a protocol

    • Several large national studies that failed to obtain biological samples for DNA extraction

  • Many options now available for obtaining DNA

  • Critical that appropriate consent is obtained for future studies and potential sample sharing


Dna extraction

DNA Extraction

Buccal brushes

Saliva

Blood draw

Guthrie card


Use of dna for studies

Use of DNA for Studies

  • DNA must be of high quality

  • Amount of DNA required varies depending on the type of application

  • Sample storage must be secure and retrieval accurate


Dna quality assessment

DNA Quality Assessment

  • A biorepository can provide assurances of DNA identity and quality

    • SNP fingerprint to ensure the correct sample is being provided

    • Relationships among samples

    • Gender validation

    • Future quality/integrity of sample

  • Future needs?

    • Race/ethnicity assessment through SNP genotyping


Clinical data set

Clinical Data Set

  • Development of a minimal clinical dataset can be very useful

    • Ensure collect critical variables for future analyses (outcome, complications, severity) using standard instruments, measures, etc

    • Relevant comorbidities to provide future broader uses of data?


Common dna studies

Common DNA Studies

  • Analyze single nucleotide polymorphisms (SNPs)

    • Limited scale or genome wide

  • Analyze DNA sequence to detect novel variation

  • Gene dosage abnormalities (deletions/ duplications)

    • Limited scale or genome wide


Snp assay

SNP Assay

  • Technology available on campus for SNP genotyping

  • Suited for moderate to large scale projects, working in 384-well format, but can accommodate smaller projects


Alcohol dependence and the adh gene cluster

ADH1C

ADH1A

ADH4

ADH5

ADH7

ADH6

ADH1B

74.9

13.8

15.2

43.4

61.4

34.6

365 kb

107 SNPs analyzed

Alcohol dependence and the ADH Gene cluster

Adapted from Howard Edenberg


Adh gene cluster

ADH Gene Cluster

Modified from Edenberg et al, 2006


Coga collaborative study on the genetics of alcoholism

COGA: Collaborative Study on the Genetics of Alcoholism

Co-Principal Investigators: B. Porjesz, V. Hesselbrock, H. Edenberg, L. Bierut

Nine centers where data collection, analysis and storage take place:

Univ. of Connecticut V. Hesselbrock

Indiana UniversityH. Edenberg, J. Nurnberger, PM Conneally, T. Foroud

University of IowaS. Kuperman, R. Crowe

SUNY HSC @ BrooklynB. Porjesz

Washington UniversityL. Bierut, A. Goate, J. Rice

Univ. of Calif. (UCSD)M. Schuckit

Howard UniversityR. Taylor

Rutgers UniversityJ. Tischfield

Southwest Foundation L. Almasy

NIAAA Staff Collaborator: M. Guo

This national collaborative study is supported by the NIH Grant U10AA008401 from the National Institute on Alcohol Abuse and Alcoholism (NIAAA) and the National Institute on Drug Abuse (NIDA). In memory of Henri Begleiter and Theodore Reich, Principal and Co-Principal Investigators of COGA since its inception. We are indebted to their leadership in the establishment and nurturing of COGA, and acknowledge with great admiration their seminal scientific contributions to the field.


Sequence variation

Sequence Variation

  • Provides ability to obtain long sequence reads, exceptional accuracy and high throughput

Bloomington: Genome Sequencer FLX (GS FLX)

Purdue: SOLiD Analyzer


National cell repository for alzheimer disease

National Cell Repository for Alzheimer Disease

NIA funded resource to make DNA and associated clinical material available to qualified researchers

U24 AG021886


Basics of ncrad

Basics of NCRAD

  • Samples from over 6,000 individuals are currently available

  • Establish lymphoblastoid cell lines (LCL) for a continuous source of DNA

  • Obtain brain tissue to confirm the AD diagnosis

    • Can also be used for additional studies

  • Detailed clinical and family history information is available from all sampled subjects


Accomplishments of ncrad

Accomplishments of NCRAD

  • Samples distributed to > 80 investigators

  • >25,000 DNA samples have been distributed to researchers

  • >1500 LCL have been distributed

  • DNA has been genotyped at central NIH laboratories and found to be of high quality

  • > 120 publications generated from these samples


Genome wide association studies

Genome Wide Association Studies


Genome wide association studies1

Genome Wide Association Studies

DNA inherited in blocks, so not all 10 million SNPs have to be tested

Genotype several hundred thousand SNPs

Controls

Cases

Compare frequency of SNP alleles in two groups

Compare frequency of SNP genotypes in two groups


What does a snp chip look like

What does a SNP Chip look like?


Copy number variation

Copy Number Variation

Increased number of copies in some samples

Data from 270 HapMap Samples on Chromosome 11


Genome wide association study in familial parkinson disease

Genome Wide Association Study in Familial Parkinson Disease

R01 NS037167


Sample demographics

Sample Demographics


Overview of data verification

Overview of Data Verification


Cryptic relatives

Cryptic Relatives

  • Despite criteria of each study to allow participation in only one genetic study, still identified related samples

    • Siblings

    • Parent-offspring


Overview of data verification1

Overview of Data Verification


Dna source

DNA Source

  • Whole genome amplified DNA

    • Overall lower genotype call rates

    • Typically between 90-95%

  • Also were able to identify samples from lymphoblastoid cell lines

    • Mosaics (i.e. partial loss of X chromosome)


Overview of data verification2

Overview of Data Verification


Progeni genepd ceph utah

PROGENI, GenePD, CEPH Utah

CEPH families are all in the main cluster

African

American

Additional Hispanics


Samples removed from analysis

Samples Removed from Analysis


Gwas results

GWAS Results

Pankratz & Wilk et al., 2008


Acknowledgements progeni

Acknowledgements- PROGENI

Indiana University

Nathan Pankratz, Ph.D.

Bernardino Ghetti, M.D.

Cheryl Halter, M.S., CCRC

Claire Wegel, M.S.

Cincinnati Children’s Hosp.

William C. Nichols, Ph.D.

Michael Pauciulo

Veronika E. Elsaesser

Diane K. Marek

Univ. of Tennessee

Ronald Pfeiffer, M.D.

University of Rochester

Alice Rudolph, Ph.D.

PSG Investigators & Coordinators

Supported by NS37167


How biorepositories can help your research1

How Biorepositories Can Help Your Research

  • Provide expertise regarding sample acquisition

  • Provide high quality DNA for genetic studies

  • Identify core resources to advance genetic hypotheses


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