Ancestrally unbiased polygenic breast cancer (BC) risk assessment.

Authors

null

Elisha Hughes

Myriad Genetics, Inc., Salt Lake City, UT

Elisha Hughes , Placede Tiemeny , Shannon Gallagher , Stephanie Meek , Charis Eng , Monique Gary , Ora Gordon , Jennifer R. Klemp , Olufunmilayo I. Olopade , Holly Jane Pederson , Jeffrey N. Weitzel , Pat W. Whitworth , Lamis Yehia , Susanne Wagner , Thomas Paul Slavin Jr., Alexander Gutin , Jerry Lanchbury

Organizations

Myriad Genetics, Inc., Salt Lake City, UT, Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH, Grand View Health, Sellersville, PA, Providence Health & Services, Renton, WA, University of Kansas Cancer Center, Westwood, KS, Center for Clinical Cancer Genetics and Global Health, University of Chicago, Chicago, IL, Medical Breast Services, Cleveland Clinic, Cleveland, OH, Latin American School of Oncology, Sierra Madre, CA, Nashville Breast Center, Nashville, TN

Research Funding

Pharmaceutical/Biotech Company
Myriad Genetics, Inc

Background: BC risk is influenced by single-nucleotide polymorphisms (SNPs) with small effects that can be aggregated into polygenic risk scores (PRSs). PRSs have primarily been developed and validated for populations of European descent. To make a PRS available for all women, we developed and validated a novel global PRS (gPRS) that utilizes individual ancestral genetic composition. Methods: Ancestry-specific PRSs corresponding to 3 continental ancestries were developed from 149 SNPs (93 BC and 56 ancestry-informative): an African PRS was developed using a cohort of 31,126 self-reported African American patients referred for hereditary cancer testing; an East Asian PRS was developed based on published data from the Asia Breast Cancer Consortium; and a European PRS was developed using data from the Breast Cancer Association Consortium and 24,259 European hereditary cancer testing patients. For each patient, ancestry-informative SNPs were used to calculate the fractional ancestry attributable to each of the 3 continents. The gPRS was the sum of ancestry specific PRSs weighted according to genetic ancestral composition. In an independent validation cohort (N = 62,707), we evaluated discrimination and calibration of gPRS, and compared performance against a previously described 86-SNP PRS for women of European ancestry. Associations of SNPs and PRSs with BC were analyzed using logistic regression adjusted for personal and family cancer history, age, and ancestry. Odds ratios (ORs) are reported per standard deviation within the corresponding patient population. P-values are reported as two-sided. Results: The gPRS was strongly associated with BC in the full validation cohort and in sub-cohorts defined by self-reported ancestry (Table). 95% (88/93) of BC SNPs had ≥1% frequency of risk alleles within each of the self-reported populations. Compared to the aforementioned 86-SNP PRS, the gPRS showed improved discrimination overall, and within each sub-cohort, with the exception of the Asian population where the sample size was too small to show superiority of either score. The 86-SNP PRS was calibrated for white non-Hispanic women but mis-calibrated for non-European ancestries. The gPRS was properly calibrated for all women. Conclusions: The 149-SNP gPRS is validated and calibrated for women of all ancestries. Combined with clinical and biological risk factors, this approach may offer improved risk stratification for all women, regardless of ancestry.

Validation Cohort
Total N
N w/ BC
OR (95% CI)
P-value
All
62,707
15,137
1.41 (1.38 – 1.44)
2.5 x 10-212
Asian
1,325
396
1.25 (1.07 - 1.45)
3.7 x 10-03
Black/African
6,743
1,754
1.23 (1.16 - 1.31)
8.5 x 10-11
Hispanic
5,847
1,066
1.35 (1.24 - 1.46)
1.6 x 10-13
Mixed Ancestry
2,681
400
1.59 (1.39 -1.82)
2.4 x 10-12
Non-European
14,959
3,435
1.29 (1.23 –1.36)
2.5 x 10-25
White and/or Ashkenazi
42,897
10,288
1.44 (1.40 – 1.48)
6.3 x 10-172

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Abstract Details

Meeting

2021 ASCO Annual Meeting

Session Type

Oral Abstract Session

Session Title

Prevention, Risk Reduction, and Hereditary Cancer

Track

Prevention, Risk Reduction, and Genetics

Sub Track

Cancer Prevention

Citation

J Clin Oncol 39, 2021 (suppl 15; abstr 10502)

DOI

10.1200/JCO.2021.39.15_suppl.10502

Abstract #

10502

Abstract Disclosures

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