Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening

Shraga, R.; Yarnall, Sarah; Elango, Sonya; Rodriguez, Sally; Bristow, Sara L.; Kumar, Neha; Niknazar, Mohammad; Hoffman, Donna L.; Ghadir, S.; Vassena, Rita; Chen, Serena H.; Hershlag, Avner; Grifo, J.; Puig, Óscar

doi:10.1101/208413

Cited by 6 publications

(11 citation statements)

References 31 publications

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“…Although self-reported race and ethnicity can be influenced by an individual's social and cultural background and, thus, may not perfectly correlate with genetic ancestry, 28 it is more reliable than assignment of race or ethnicity by another person (e.g., a healthcare professional). 29 However, it should be noted that self-reported measures can be complicated by collection processes, 30 including an incomplete selection of possible identity categories or allowing only one selection and thus failing to capture whether an individual may identify with multiple categories or none at all. 29 These classification limitations can be particularly prevalent among populations with a high degree of admixture.…”

Section: Admixed Populationsmentioning

confidence: 99%

Standardized Biogeographic Grouping System for Annotating Populations in Pharmacogenetic Research

Huddart

Fohner

Whirl‐Carrillo

et al. 2019

Clin Pharma and Therapeutics

117

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The varying frequencies of pharmacogenetic alleles among populations have important implications for the impact of these alleles in different populations. Current population grouping methods to communicate these patterns are insufficient as they are inconsistent and fail to reflect the global distribution of genetic variability. To facilitate and standardize the reporting of variability in pharmacogenetic allele frequencies, we present seven geographically defined groups: American, Central/South Asian, East Asian, European, Near Eastern, Oceanian, and Sub‐Saharan African, and two admixed groups: African American/Afro‐Caribbean and Latino. These nine groups are defined by global autosomal genetic structure and based on data from large‐scale sequencing initiatives. We recognize that broadly grouping global populations is an oversimplification of human diversity and does not capture complex social and cultural identity. However, these groups meet a key need in pharmacogenetics research by enabling consistent communication of the scale of variability in global allele frequencies and are now used by Pharmacogenomics Knowledgebase (PharmGKB).

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Section: Admixed Populationsmentioning

confidence: 99%

Standardized Biogeographic Grouping System for Annotating Populations in Pharmacogenetic Research

Huddart

Fohner

Whirl‐Carrillo

et al. 2019

Clin Pharma and Therapeutics

117

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“…5 In addition, self-reported ethnicity is not a reliable tool for clinical decision-making. 6 Given the problems with ethnic-based screening and improvements in technology, Expanded Carrier Screening (ECS) panels have become a viable option. Compared to ethnicity-based screening, ECS can evaluate 100 of variants associated with genetic disease.…”

Section: Introductionmentioning

confidence: 99%

“…However, this ethnicity‐based screening has problems, such as an increased rate of mixed racial ancestry, patient preferences against the use of racial categorization in medicine, and the possibility of unknown ancestry 5 . In addition, self‐reported ethnicity is not a reliable tool for clinical decision‐making 6 . Given the problems with ethnic‐based screening and improvements in technology, Expanded Carrier Screening (ECS) panels have become a viable option.…”

Section: Introductionmentioning

confidence: 99%

Reproductive male partner testing when the female is identified to be a genetic disease carrier

et al. 2020

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Objective To quantify carrier testing uptake rates for male partners of women found to be a carrier(s) for autosomal recessive conditions and to understand reasons for declining testing (uptake rate). Methods A retrospective chart review of 513 female patients seen at Rutgers‐Robert Wood Johnson Medical School found to be carriers through expanded carrier screening (ECS) panels. The aims of this study were to determine how often their male partner chose testing, reasons for declining and the type of methodology chosen for their screening. Results Male partner uptake rate was 77%. We identified that the most significant barrier to male partner testing is female patients not following up on their own carrier screening results, thus missing the opportunity for partner testing. When male partners were provided options for testing, the most reported reason for declining is the belief it would have no impact on pregnancy management (20%). A carrier couple rate of 8.3% was identified of partners tested. Conclusion Despite a relatively high male testing uptake rate, a quarter of carrier females did not proceed with testing their partner. To ascertain fetal risk, results for both parents is necessary. Pretest counseling should stress need for potential male partner follow‐up testing.

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“…In addition, many pharmacogenetic-variant alleles have frequencies that vary across ethnicities. 39 As self-reported ethnicity is not always in agreement with genetic ethnicity, 40 it is of clinical importance that the PGx-Passport contains all variant alleles that are considered common in at least one defined ethnicity. For example, CYP2D6*6 has a global MAF < 1% but an MAF of 2% in Europeans and was, therefore, selected to be included in the panel.…”

Section: Discussionmentioning

confidence: 99%

Development of the PGx‐Passport: A Panel of Actionable Germline Genetic Variants for Pre‐Emptive Pharmacogenetic Testing

Wouden

Rhenen

Jama

et al. 2019

Clin Pharma and Therapeutics

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Pre‐emptive pharmacogenetics (PGx) testing of a panel of germline genetic variants represents a new model for personalized medicine. Clinical impact of PGx testing is maximized when all variant alleles for which actionable clinical guidelines are available are included in the test panel. However, no such standardized panel has been presented to date, impeding adoption, exchange, and continuity of PGx testing. We, therefore, developed such a panel, hereafter called the PGx‐Passport, based on the actionable Dutch Pharmacogenetics Working Group (DPWG) guidelines. Germline‐variant alleles were systematically selected using predefined criteria regarding allele population frequencies, effect on protein functionality, and association with drug response. A PGx‐Passport of 58 germline variant alleles, located within 14 genes (CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A5, DPYD, F5, HLA‐A, HLA‐B, NUDT15, SLCO1B1, TPMT, UGT1A1, and VKORC1) was composed. This PGx‐Passport can be used in combination with the DPWG guidelines to optimize drug prescribing for 49 commonly prescribed drugs.

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Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening

Abstract: Background: Current professional society guidelines recommend genetic carrier screening be

Cited by 6 publications

References 31 publications

Standardized Biogeographic Grouping System for Annotating Populations in Pharmacogenetic Research

Standardized Biogeographic Grouping System for Annotating Populations in Pharmacogenetic Research

Reproductive male partner testing when the female is identified to be a genetic disease carrier

Development of the PGx‐Passport: A Panel of Actionable Germline Genetic Variants for Pre‐Emptive Pharmacogenetic Testing

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