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Morgan J, Coe RR, Lesueur R, Kenny R, Price R, Makela N, Birch PH. Indigenous Peoples and genomics: Starting a conversation. J Genet Couns 2018; 28:407-418. [PMID: 30629780 PMCID: PMC7379939 DOI: 10.1002/jgc4.1073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/30/2018] [Accepted: 11/06/2018] [Indexed: 12/16/2022]
Abstract
Compared to European ancestral groups, Indigenous Canadians are more likely to have uninterpretable genome-wide sequencing results due to non-representation in reference databases. We began a conversation with Indigenous Canadians to raise awareness and give voice to this issue. We co-created a video explaining genomic non-representation that included diverse Indigenous view-points. We audio-recorded the focus groups including 30 First Nations, Métis, and Inuit individuals living in Greater Vancouver. After watching an introductory video explaining genomic testing, participants discussed issues surrounding collecting Indigenous genomic data, its control, and usage. Transcripts were analyzed, and participants' quotes representing main themes were incorporated into the introductory video. Indigenous participants discussed data interpretation and gave approval for quote usage. The 20 participants who provided feedback concurred with the thematic interpretation: Systemic racism interlaced most conversations, particularly within the theme of trust. Themes of governance emphasized privacy and fear of discrimination. Some participants thought a separate, Indigenous-controlled database was essential; others recognized advantages of international databases. The theme of implementation included creative ideas to collect Indigenous genomes, but prior approval from Indigenous leaders was emphasized. The final video (https://youtu.be/-wivIBDjoi8) was shared with participants to use as they wish to promote awareness and ongoing discussion of genomic diagnostic inequity.
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Affiliation(s)
- Jenny Morgan
- Indigenous Health Program, BC Women's and Children's Hospitals, Vancouver, BC, Canada
| | - Rachel R Coe
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Rochelle Lesueur
- Indigenous Health Program, BC Women's and Children's Hospitals, Vancouver, BC, Canada
| | - Ruth Kenny
- Indigenous Health Program, BC Women's and Children's Hospitals, Vancouver, BC, Canada
| | - Roberta Price
- Indigenous Health Program, BC Women's and Children's Hospitals, Vancouver, BC, Canada
| | - Nancy Makela
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Patricia H Birch
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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Zahir FR, Mwenifumbo JC, Chun HJE, Lim EL, Van Karnebeek CDM, Couse M, Mungall KL, Lee L, Makela N, Armstrong L, Boerkoel CF, Langlois SL, McGillivray BM, Jones SJM, Friedman JM, Marra MA. Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability. BMC Genomics 2017; 18:403. [PMID: 28539120 PMCID: PMC5442678 DOI: 10.1186/s12864-017-3671-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Intellectual Disability (ID) is among the most common global disorders, yet etiology is unknown in ~30% of patients despite clinical assessment. Whole genome sequencing (WGS) is able to interrogate the entire genome, providing potential to diagnose idiopathic patients. METHODS We conducted WGS on eight children with idiopathic ID and brain structural defects, and their normal parents; carrying out an extensive data analyses, using standard and discovery approaches. RESULTS We verified de novo pathogenic single nucleotide variants (SNV) in ARID1B c.1595delG and PHF6 c.820C > T, potentially causative de novo two base indels in SQSTM1 c.115_116delinsTA and UPF1 c.1576_1577delinsA, and de novo SNVs in CACNB3 c.1289G > A, and SPRY4 c.508 T > A, of uncertain significance. We report results from a large secondary control study of 2081 exomes probing the pathogenicity of the above genes. We analyzed structural variation by four different algorithms including de novo genome assembly. We confirmed a likely contributory 165 kb de novo heterozygous 1q43 microdeletion missed by clinical microarray. The de novo assembly resulted in unmasking hidden genome instability that was missed by standard re-alignment based algorithms. We also interrogated regulatory sequence variation for known and hypothesized ID genes and present useful strategies for WGS data analyses for non-coding variation. CONCLUSION This study provides an extensive analysis of WGS in the context of ID, providing genetic and structural insights into ID and yielding diagnoses.
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Affiliation(s)
- Farah R Zahir
- Canada's Michael Smith Genome Sciences Center, Vancouver, BC, V5Z 4S6, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. .,Qatar Biomedical Research Institute, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar.
| | - Jill C Mwenifumbo
- Canada's Michael Smith Genome Sciences Center, Vancouver, BC, V5Z 4S6, Canada
| | - Hye-Jung E Chun
- Canada's Michael Smith Genome Sciences Center, Vancouver, BC, V5Z 4S6, Canada
| | - Emilia L Lim
- Canada's Michael Smith Genome Sciences Center, Vancouver, BC, V5Z 4S6, Canada
| | - Clara D M Van Karnebeek
- Department of Pediatrics, Centre for Molecular Medicine & Therapeutics Child & Family Research Institute, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Madeline Couse
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Center, Vancouver, BC, V5Z 4S6, Canada
| | - Leora Lee
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nancy Makela
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Linlea Armstrong
- Provincial Medical Genetics Programme, Children's & Women's Health Centre of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Cornelius F Boerkoel
- Provincial Medical Genetics Programme, Children's & Women's Health Centre of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Sylvie L Langlois
- Provincial Medical Genetics Programme, Children's & Women's Health Centre of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Barbara M McGillivray
- Provincial Medical Genetics Programme, Children's & Women's Health Centre of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Center, Vancouver, BC, V5Z 4S6, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Center, Vancouver, BC, V5Z 4S6, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Ashtiani S, Makela N, Carrion P, Austin J. Parents' experiences of receiving their child's genetic diagnosis: a qualitative study to inform clinical genetics practice. Am J Med Genet A 2014; 164A:1496-502. [PMID: 24706543 DOI: 10.1002/ajmg.a.36525] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/28/2014] [Indexed: 11/07/2022]
Abstract
Little is currently known about how parents experience the medical genetics appointment at which their child receives a genetic diagnosis. We conducted semi-structured in-person interviews with 13 parents of 10 index children to explore their experience in the medical genetics appointment in which they received their child's genetic diagnosis. Guided by grounded theory, we used a constant comparative approach to data analysis. Transcribed interviews were coded and sorted, and thematic categories identified. Sixty-one and a half percent of parents experienced the diagnosis session as negative, 23% felt the experience was positive, and 15.5% were ambivalent. Receiving emotional support, an outline of the follow-up plans, and messages of hope and perspective during the session seemed to positively influence parents' experience, while feeling that their role was as a passive receiver of information and the use of difficult medical terminology negatively influenced parents' overall experience. Parental preparedness for the information, and the parents' emotional reaction to the diagnosis were also factors that influenced the parental experience. Few participants understood the role of the genetic counselor. Our results provide in-depth insight into the parental experience of the pediatric medical genetics diagnosis session. We propose a mechanism through which parental experience shapes their perception of the medical genetics session.
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Affiliation(s)
- Setareh Ashtiani
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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Regier DA, Friedman JM, Makela N, Ryan M, Marra CA. Valuing the benefit of diagnostic testing for genetic causes of idiopathic developmental disability: willingness to pay from families of affected children. Clin Genet 2009; 75:514-21. [PMID: 19508416 DOI: 10.1111/j.1399-0004.2009.01193.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Idiopathic developmental disability (DD) has been found to put significant psychological distress on families of children with DD. The cause of the disability, however, is unknown for up to one-half of the affected children. Chromosomal abnormalities identified by cytogenetic analysis are the most frequently recognized cause of DD, although they account for less than 10% of cases. Array genomic hybridization (AGH) is a new diagnostic tool that provides a much higher detection rate for chromosomal imbalance than conventional cytogenetic analysis. This increase in diagnostic capability comes at greater monetary costs, which provides an impetus for understanding how individuals value genetic testing for DD. This study estimated the willingness to pay (WTP) for diagnostic testing to find a genetic cause of DD from families of children with DD. A discrete choice experiment was used to obtain WTP values. When it was assumed that AGH resulted in twice as many diagnoses and a 1-week reduction in waiting time compared with conventional cytogenetic analysis, this study found that families were willing to pay up to CDN$1118 (95% confidence interval, $498-1788) for the expected benefit. These results support the conclusion that the introduction of AGH into the Canadian health care system may increase the perceived welfare of society, but future studies should examine the cost-benefit of AGH vs cytogenetic testing.
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Affiliation(s)
- D A Regier
- National Perinatal Epidemiology Unit, University of Oxford, Oxford, UK.
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