Scientific Understanding & Technical Capabilities

This theme relates to increasing the scientific understanding of genetics and genomics and how that knowledge can be utilised in medicine as well as improving the technical aspects of genomics such as developing sequencing capabilities. 

Issues

Within the Catalogue of Global Genomic Medicine Implementation Initiatives, almost all of the initiatives (56/61)* gave some acknowledgement to increasing scientific understanding and technical capabilities and the following types of activities were described:

Scientific understanding

  • understanding the genetic diversity of different population groups (enhancing the diversity of reference databases)

  • understanding the genetic causes of disease and patterns of predisposition to disease from rare Mendelian to common complex disorders

  • re-classifying diseases at the molecular level

  • identifying clinically relevant disease subtypes

  • conducting association studies

  • broadening understanding about gene expression and regulation

  • defining biomarkers and therapeutic targets

  • supporting research in preclinical models, biomarker evaluation and validation processes

  • systems biology approaches and experiments in suitable disease/ animal models

  • applying genomics to early detection, prevention and management of disease

  • understanding drug responses

  • developing new clinical trial designs and promoting integration with preclinical testing

  • developing new stem cell therapies

  • studying correlations between specific diseases and the composition of the microbiome

Technical capabilities

  • building genomic and bioinformatics facilities 

  • developing and integrating clinical phenotyping capabilities

  • sample collection processes and biobanking infrastructure

  • functional analysis capabilities

  • creating genomics networks and reference centres

  • granting access to cutting edge research equipment

  • developing methods for integration and evaluation of information from genomic, epigenetic, transcriptomic, proteomic, metabolomic and microbiome analyses

  • embedding implementation research (including cost effectiveness) at all stages of service redevelopment and laboratory reconfiguration

In addition to work within the initiatives in the catalogue there are also other entities that are interested in promoting new scientific understanding and technical capabilities. A number of networks and collaborations are supporting this activity by providing access to resources such as data, samples, clinical information, variant browsers, gen-phen databases and more. Links to a number of these entities are provided.

Resources on scientific understanding and technical capabilities:

Scholarly articles on ethnic-specific clinical and genomic data

Peña-Chilet M, Roldán G, Perez-Florido J, Ortuño FM, Carmona R, Aquino V, et al. CSVS, a crowdsourcing database of the Spanish population genetic variability. Nucleic Acids Research. 2020. https://doi.org/10.1093/nar/gkaa794

Pemmasani SK, Raman R, Mohapatra R, Vidyasagar M, Acharya A. A Review on the Challenges in Indian Genomics Research for Variant Identification and Interpretation. Frontiers in genetics. 2020;11:753-. https://doi.org/10.3389/fgene.2020.00753

Ishigaki K, Akiyama M, Kanai M, Takahashi A, Kawakami E, Sugishita H, et al. Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases. Nature Genetics. 2020;52(7):669-79. https://doi.org/10.1038/s41588-020-0640-3

Mayer AK, Balousha G, Sharkia R, Mahajnah M, Ayesh S, Schulze M, et al. Unraveling the genetic cause of hereditary ophthalmic disorders in Arab societies from Israel and the Palestinian Authority. European Journal of Human Genetics. 2020;28(6):742-53. https://doi.org/10.1038/s41431-019-0566-3

Sherman RM, Salzberg SL. Pan-genomics in the human genome era. Nature Reviews Genetics. 2020;21(4):243-54. https://doi.org/10.1038/s41576-020-0210-7

Radouani F, Zass L, Hamdi Y, Rocha Jd, Sallam R, Abdelhak S, et al. A review of clinical pharmacogenetics Studies in African populations. Personalized Medicine. 2020. https://doi.org/10.2217/pme-2019-0110

Ye D, Jiang D, Gu S, Mao Y, Qian S, Lin S, et al. Evaluating the predictive value of genetic risk score in colorectal cancer among Chinese Han population. Journal of Human Genetics. 2020;65(3):271-9. https://doi.org/10.1038/s10038-019-0703-4

Zambrano-Mila MS, Agathos SN, Reichardt JKV. Human genetics and genomics research in Ecuador: historical survey, current state, and future directions. Human Genomics. 2019;13(1):64. https://doi.org/10.1186/s40246-019-0249-8

Fthenou E, Al Thani A, Al Marri A, Afifi N. Qatar Biobank: A Paradigm of Translating Biobank Science into Evidence-Based Health Care Interventions. Biopreservation and Biobanking. 2019;17(6):491-3. https://doi.org/10.1089/bio.2019.0051

Zlotogora J. The Israeli national population program of genetic carrier screening for reproductive purposes. How should it be continued? Israel Journal of Health Policy Research. 2019;8(1):73. https://doi.org/10.1186/s13584-019-0345-1

Wall JD, Stawiski EW, Ratan A, Kim HL, Kim C, Gupta R, et al. The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature. 2019;576(7785):106-11. https://doi.org/10.1038/s41586-019-1793-z

Wu D, Dou J, Chai X, Bellis C, Wilm A, Shih CC, et al. Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore. Cell. 2019;179(3):736-49.e15. https://doi.org/10.1016/j.cell.2019.09.019

Manolio TA. Using the Data We Have: Improving Diversity in Genomic Research. The American Journal of Human Genetics. 2019;105(2):233-6. https://doi.org/10.1016/j.ajhg.2019.07.008

Bylstra Y, Davila S, Lim WK, Wu R, Teo JX, Kam S, et al. Implementation of genomics in medical practice to deliver precision medicine for an Asian population. npj Genomic Medicine. 2019;4(1):12. https://doi.org/10.1038/s41525-019-0085-8

Bylstra Y, Kuan JL, Lim WK, Bhalshankar JD, Teo JX, Davila S, et al. Population genomics in South East Asia captures unexpectedly high carrier frequency for treatable inherited disorders. Genet Med. 2019;21(1):207-12. https://doi.org/10.1038/s41436-018-0008-6

Le VS, Tran KT, Bui HTP, Le HTT, Nguyen CD, Do DH, et al. A Vietnamese human genetic variation database. Human Mutation. 2019; Epub ahead of print. https://doi.org/10.1002/humu.23835

Morales J, Welter D, Bowler EH, Cerezo M, Harris LW, McMahon AC, et al. A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. Genome Biol. 2018;19(1):21. https://doi.org/10.1186/s13059-018-1396-2

Al-Ali M, Osman W, Tay GK, AlSafar HS. A 1000 Arab genome project to study the Emirati population. J Hum Genet. 2018;63(4):533-6. https://doi.org/10.1038/s10038-017-0402-y

Van den Eynden J, Descamps T, Delporte E, Roosens NHC, De Keersmaecker SCJ, De Wit V, et al. The genetic structure of the Belgian population. Human Genomics. 2018;12(1):6. https://doi.org/10.1186/s40246-018-0136-8

Lan T, Lin H, Zhu W, Laurent TCAM, Yang M, Liu X, et al. Deep whole-genome sequencing of 90 Han Chinese genomes. GigaScience. 2017;6(9). https://doi.org/10.1093/gigascience/gix067

Ameur A, Dahlberg J, Olason P, Vezzi F, Karlsson R, Martin M, et al. SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population. European Journal Of Human Genetics. 2017;25:1253. https://doi.org/10.1038/ejhg.2017.130 

Qasim I, Ahmad B, Khan MA, Khan N, Muhammad N, Basit S, et al. Pakistan Genetic Mutation Database (PGMD); A centralized Pakistani mutome data source. European Journal of Medical Genetics. 2017. https://doi.org/10.1016/j.ejmg.2017.11.015

Fakhro KA, Staudt MR, Ramstetter MD, Robay A, Malek JA, Badii R, et al. The Qatar genome: a population-specific tool for precision medicine in the Middle East. Hum Genome Var. 2016;3:16016. https://doi.org/10.1038/hgv.2016.16

Thareja G, John SE, Hebbar P, Behbehani K, Thanaraj TA, Alsmadi O. Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry. BMC Genomics. 2015;16:92. https://doi.org/10.1186/s12864-015-1233-x

Zhang W, Meehan J, Su Z, Ng HW, Shu M, Luo H, et al. Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population. BMC Bioinformatics. 2014;15 Suppl 11:S6. https://doi.org/10.1186/1471-2105-15-S11-S6

Ling Y, Jin Z, Su M, Zhong J, Zhao Y, Yu J, et al. VCGDB: a dynamic genome database of the Chinese population. BMC Genomics. 2014;15:265. https://doi.org/10.1186/1471-2164-15-265

Wong L-P, Ong Rick T-H, Poh W-T, Liu X, Chen P, Li R, et al. Deep Whole-Genome Sequencing of 100 Southeast Asian Malays. The American Journal of Human Genetics. 2013;92(1):52-66. https://doi.org/10.1016/j.ajhg.2012.12.005

IGSR: The International Genome Sample Resource http://www.internationalgenome.org/home

1000 Genomes Project Publications

Pilot Analysis

1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, et al. A map of human genome variation from population-scale sequencing. Nature. 2010;467(7319):1061-73. https://doi.org/10.1038/nature09534

Phase 1 Analysis

1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491(7422):56-65.https://doi.org/10.1038/nature11632

Phase 3 Analysis

1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. 2015;526(7571):68-74. https://doi.org/10.1038/nature15393

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 2015;526(7571):75-81. https://doi.org/10.1038/nature15394

* Initiatives from the catalogue that acknowledge scientific education and technical capability themes

Africa (2) - Human Heredity and Health in Africa (H3Africa) White Paper, Human Heredity and Health in Africa (H3Africa) Initiative

Argentina (1) -Precision Medicine Initiative Grant

Asia (1) -GenomeAsia 100k

Australia (8) - National Health Genomics Policy Framework, NSW Health Genomics Strategy, Genetic and genomic healthcare for Victoria 2021, Australian Genomics, Melbourne Genomics Health Alliance, Queensland Genomics Health Alliance, South Australian Genomics Health Alliance,Australian Genomics Health Futures Mission

Belgium (1)– Genomics and Public Health in Belgium

Brazil (2) -Brazilian Initiative on Precision Medicine (BIPMed), Human Genome and Stem-Cell Research Center (HUG-CEL)

Canada (5) – Genome Canada Strategic Plan 2012-2017, Genome Canada, Genome BC - Strategy for Genomics in the Health Sector in British Columbia, CanDIG-Canadian Distributed Infrastructure for Genomics, Genome Canada National Initiative for the Clinical Implementation of Precision Health

China – Hong Kong (1)- Hong Kong Genome Project

Denmark (2) -National Strategy for Personalised Medicine 2017-2020,GenomeDenmark platform

Estonia (1) -Estonian Genome Center of the University of Tartu (EGCUT) Development Plan for 2015-2021

Europe (2) -Shaping Europe’s Vision for Personalised Medicine - Strategic Research and Innovation Agenda (SRIA), Ubiquitous Pharmacogenomics (U-PGx)

Finland (2) - Improving Health through the use of Genomic Data, FINNGEN

France (1) - French Plan for Genomic Medicine 2025 

India (2) -National Biotechnology Development Strategy, GenomeIndia initiative

Iran (1) - Iranome

Italy (1) - National Plan for Public Health Genomics

Japan (1) - Implementation of Genomic Medicine Project

Mexico (1) - Promotional Consortium of the National Institute of Genomic Medicine (INMEGEN)

Middle East (2) - Centre for Arab Genomic Studies, Dubai Genomics

Netherlands (1) -Genome of the Netherlands (GoNL)

New Zealand (1) -Genomics Aotearoa

Philippines (1) -Philippine Genome Center (PGC)

Qatar (1) -Qatar Genome Programme (QGP)

Saudia Arabia (1) -Saudi Human Genome Program

Singapore (1) -POLARIS (Personalized OMIC Lattice for Advanced Research and Improving Stratification) 

South Africa (1) -Southern African Human Genome Programme (SAHGP)

South Korea (1) -Genomic Medicine in Korea: Plan and Infrastructure Genome Technology to Business Translation Program

Spain (1) - CIBERER (Center for Network Research on Rare Diseases)

Sweden (1) -SweGen project

Thailand (2) -Thailand’s National Biotechnology Policy Framework (2012-2021), Genomics Thailand

Turkey (1) -Turkish genome project

United Kingdom (3) - Building on our inheritance - Genomic technology in healthcare, The 100,000 Genomes Project Protocol, Generation Genome- Annual Report of the Chief Medical Officer 2016

USA (2) -The 2011 NHGRI strategic plan - Charting a course for genomic medicine from base pairs to bedside, All of Us (Precision Medicine Initiative), Project Baby Bear

The development of these resources was supported by the Global Genomic Medicine Initiative (G2MC) and the Australian Genomics Health Alliance (Australian Genomics)