Large Scale Genomics

Question 1

Biobank Outline

Answer 1

Large biospecimen collection linked to personal health (genetics, healthcare records, family history). Legal entity driving collection, preservation, preservation, testing, analysing & distributing bio data. Created by -omics technologies

Question 2

Biobank Data Types

Answer 2

Genetic data, Omics, Biomarkers, Health records, Activity monitoring (eg heart rate), Scanning data, Test results, Physical attributes & Family history

Question 3

Biobank Roles

Answer 3

Collection & storage of bio/medical data, Natural progression measure (continuous monitoring), Research, Anonymity settings and Consent models

Question 4

2 Biobank Types

Answer 4

Population based and Disease-oriented based

Question 5

Population Based Biobank

Answer 5

Captures info of entire population, lacks power for rare disease (rarity correlates power). Generates controls for disease genotype identification. Future oriented. Eg; UK Biobank

Question 6

Disease-oriented Based Biobank

Answer 6

Captures info of rare disease population (small sample size). Cost effective. Eg; AIDS

Question 7

Biobank Size

Answer 7

3,000-5,000 disease cases minimum with 3 times as many controls (modest effect eval)

Question 8

Age Balance For Biobank Late Onset Diseases

Answer 8

Individuals must be old enough to develop disease in reasonable timeframe but young enough to measure risk factors before disease onset. Typically ~40

Question 9

How biobank is Formed

Answer 9

Medics, biologists, bioethicists, bioinformatics, administrators and ID collect data. Funding sourcing and cost eval. Ensures regulatory compliance is adhered to

Question 10

Laboratory Information Management Systems (LIMS)

Answer 10

Software for managing (collate, store, sort & retrieve) samples. Can track and access samples for biobank lifecycle

Question 11

Psuedonymisation Outline

Answer 11

Not true anonymisation. Info replaced by codes but with accessible documentation linking code with info. Subject to strict info

Question 12

Data Standardisation Outline

Answer 12

Allows data to be shared between biobanks. Standardise enviornments for collection and storage (same readings). From US National Cancer Human Biobank

Question 13

Biobank Protocols

Answer 13

Standard Operating Procedures (SOPs)

Question 14

Bioethics Outline

Answer 14

Biobank ownership of personal samples need to be consented. 2 types consent: broad and dynamic

Question 15

Broad Consent Outline

Answer 15

1 off consent process. Clearly defines acceptable research topics for donated samples

Question 16

Dynamic Consent Outline

Answer 16

Routine check-in with participants. Ensure consent is continued with different research tastes

Question 17

Components of Informed Consent

Answer 17

Freely given, specific, unambiguous, understandable language, distinguishable. Must be given in a clear statement or action (signing)

Question 18

Data Access Outline

Answer 18

Biobanks decide who allows access. Give to bona fide researchers as long as it has positive health impact. Management of perishable materials

Question 19

Stages of Biobank Lifecycle

Answer 19

Collection, Accession, Preservation, Long-term storage, Quality control, Transport and Disposal

Question 20

UK Biobanks

Answer 20

500,000 middle age (40+) participants. Autosomal SNPs, GWAS, Polygenic Risk Scores. Has individuals of non-European Ancestry. Discovered: MAP3K15 diabetic protective mutation, PRS for BMI

Question 21

All of Us Program

Answer 21

US 1 million participants 18+, diversity as tenant. Research transparency

Question 22

Qatar Biobank Outline

Answer 22

60,000 participants 18+ (all Quatari citisens eligible). Improved diabeted stratification

Question 23

H3 Africa Outline

Answer 23

70,000 participants from 22 countries in African country. Fine mapping of lipid loci

Question 24

Baby Seq Project Outline

Answer 24

Randomised trial of genome sequence benefits in newborns (test and control group). 200 newborns

Question 25

Genome of Ireland Outline

Answer 25

Forming of biobank for modern Irish genomes