Deep sequencing across germline genome-wide association study signals relating to breast cancer events in women receiving aromatase inhibitors for adjuvant therapy of early breast cancer

James N. Ingle, Krishna R. Kalari, Yukihide Momozawa, Michiaki Kubo, Yoichi Furukawa, Lois E. Shepherd, Matthew J. Ellis, Paul E. Goss, Poulami Barman, Erin E. Carlson, Jason P. Sinnwell, Xiaojia Tang, Matthew P. Goetz, Bingshu E. Chen, Junmei Cairns, Richard M. Weinshilboum, Liewei Wang

Research output: Contribution to journalArticle

Abstract

OBJECTIVE: To identify additional genetic variants beyond those observed in a previous genome-wide association study (GWAS) in women treated on the MA.27 clinical trial in which women were randomized to 5 years of adjuvant therapy with anastrozole or exemestane. PATIENTS AND METHODS: We performed a matched case-control study in 234 women who had a recurrence of breast cancer (cases) and 649 women who had not (controls). The analysis was restricted to White women with an estrogen receptor-positive breast cancer. Multiplex PCR-based targeted deep sequencing was performed of the MIR2052HG region on chromosome 8 between positions 75.4 and 75.7, a span of 300 kb, in an attempt to identify additional functional single nucleotide polymorphisms (SNPs). RESULTS: A total of 4677 unique variants were identified that had not been identified in the previous GWAS. Clinical Annotation of Variants analysis revealed 10 variants, including eight SNPs and two insertion-deletion mutations with moderate or high impact. However, none of the common and variant regions was significant after adjustment for the most significant SNP (rs13260300) identified in our previous GWAS. We performed haplotype analysis that revealed two regions in which the haplotypes lost significance when adjusted for this prior GWAS SNP and one region with two significant haplotypes (P = 0.046 and 0.031) after adjusting for the GWAS SNP. CONCLUSION: We were unable to identify common or rare variant regions that added value to the findings from our previous GWAS. We did find two haplotypes that were significant after adjusting for our top GWAS SNP but these were considered to be of marginal value.

Original languageEnglish
Pages (from-to)183-191
Number of pages9
JournalPharmacogenetics and genomics
Volume29
Issue number8
DOIs
Publication statusPublished - 01-10-2019

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High-Throughput Nucleotide Sequencing
Aromatase Inhibitors
Genome-Wide Association Study
Single Nucleotide Polymorphism
Breast Neoplasms
Haplotypes
exemestane
Therapeutics
INDEL Mutation
Chromosomes, Human, Pair 8
Multiplex Polymerase Chain Reaction
Estrogen Receptors
Case-Control Studies
Clinical Trials
Recurrence

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

Ingle, James N. ; Kalari, Krishna R. ; Momozawa, Yukihide ; Kubo, Michiaki ; Furukawa, Yoichi ; Shepherd, Lois E. ; Ellis, Matthew J. ; Goss, Paul E. ; Barman, Poulami ; Carlson, Erin E. ; Sinnwell, Jason P. ; Tang, Xiaojia ; Goetz, Matthew P. ; Chen, Bingshu E. ; Cairns, Junmei ; Weinshilboum, Richard M. ; Wang, Liewei. / Deep sequencing across germline genome-wide association study signals relating to breast cancer events in women receiving aromatase inhibitors for adjuvant therapy of early breast cancer. In: Pharmacogenetics and genomics. 2019 ; Vol. 29, No. 8. pp. 183-191.
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abstract = "OBJECTIVE: To identify additional genetic variants beyond those observed in a previous genome-wide association study (GWAS) in women treated on the MA.27 clinical trial in which women were randomized to 5 years of adjuvant therapy with anastrozole or exemestane. PATIENTS AND METHODS: We performed a matched case-control study in 234 women who had a recurrence of breast cancer (cases) and 649 women who had not (controls). The analysis was restricted to White women with an estrogen receptor-positive breast cancer. Multiplex PCR-based targeted deep sequencing was performed of the MIR2052HG region on chromosome 8 between positions 75.4 and 75.7, a span of 300 kb, in an attempt to identify additional functional single nucleotide polymorphisms (SNPs). RESULTS: A total of 4677 unique variants were identified that had not been identified in the previous GWAS. Clinical Annotation of Variants analysis revealed 10 variants, including eight SNPs and two insertion-deletion mutations with moderate or high impact. However, none of the common and variant regions was significant after adjustment for the most significant SNP (rs13260300) identified in our previous GWAS. We performed haplotype analysis that revealed two regions in which the haplotypes lost significance when adjusted for this prior GWAS SNP and one region with two significant haplotypes (P = 0.046 and 0.031) after adjusting for the GWAS SNP. CONCLUSION: We were unable to identify common or rare variant regions that added value to the findings from our previous GWAS. We did find two haplotypes that were significant after adjusting for our top GWAS SNP but these were considered to be of marginal value.",
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Ingle, JN, Kalari, KR, Momozawa, Y, Kubo, M, Furukawa, Y, Shepherd, LE, Ellis, MJ, Goss, PE, Barman, P, Carlson, EE, Sinnwell, JP, Tang, X, Goetz, MP, Chen, BE, Cairns, J, Weinshilboum, RM & Wang, L 2019, 'Deep sequencing across germline genome-wide association study signals relating to breast cancer events in women receiving aromatase inhibitors for adjuvant therapy of early breast cancer', Pharmacogenetics and genomics, vol. 29, no. 8, pp. 183-191. https://doi.org/10.1097/FPC.0000000000000382

Deep sequencing across germline genome-wide association study signals relating to breast cancer events in women receiving aromatase inhibitors for adjuvant therapy of early breast cancer. / Ingle, James N.; Kalari, Krishna R.; Momozawa, Yukihide; Kubo, Michiaki; Furukawa, Yoichi; Shepherd, Lois E.; Ellis, Matthew J.; Goss, Paul E.; Barman, Poulami; Carlson, Erin E.; Sinnwell, Jason P.; Tang, Xiaojia; Goetz, Matthew P.; Chen, Bingshu E.; Cairns, Junmei; Weinshilboum, Richard M.; Wang, Liewei.

In: Pharmacogenetics and genomics, Vol. 29, No. 8, 01.10.2019, p. 183-191.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Deep sequencing across germline genome-wide association study signals relating to breast cancer events in women receiving aromatase inhibitors for adjuvant therapy of early breast cancer

AU - Ingle, James N.

AU - Kalari, Krishna R.

AU - Momozawa, Yukihide

AU - Kubo, Michiaki

AU - Furukawa, Yoichi

AU - Shepherd, Lois E.

AU - Ellis, Matthew J.

AU - Goss, Paul E.

AU - Barman, Poulami

AU - Carlson, Erin E.

AU - Sinnwell, Jason P.

AU - Tang, Xiaojia

AU - Goetz, Matthew P.

AU - Chen, Bingshu E.

AU - Cairns, Junmei

AU - Weinshilboum, Richard M.

AU - Wang, Liewei

PY - 2019/10/1

Y1 - 2019/10/1

N2 - OBJECTIVE: To identify additional genetic variants beyond those observed in a previous genome-wide association study (GWAS) in women treated on the MA.27 clinical trial in which women were randomized to 5 years of adjuvant therapy with anastrozole or exemestane. PATIENTS AND METHODS: We performed a matched case-control study in 234 women who had a recurrence of breast cancer (cases) and 649 women who had not (controls). The analysis was restricted to White women with an estrogen receptor-positive breast cancer. Multiplex PCR-based targeted deep sequencing was performed of the MIR2052HG region on chromosome 8 between positions 75.4 and 75.7, a span of 300 kb, in an attempt to identify additional functional single nucleotide polymorphisms (SNPs). RESULTS: A total of 4677 unique variants were identified that had not been identified in the previous GWAS. Clinical Annotation of Variants analysis revealed 10 variants, including eight SNPs and two insertion-deletion mutations with moderate or high impact. However, none of the common and variant regions was significant after adjustment for the most significant SNP (rs13260300) identified in our previous GWAS. We performed haplotype analysis that revealed two regions in which the haplotypes lost significance when adjusted for this prior GWAS SNP and one region with two significant haplotypes (P = 0.046 and 0.031) after adjusting for the GWAS SNP. CONCLUSION: We were unable to identify common or rare variant regions that added value to the findings from our previous GWAS. We did find two haplotypes that were significant after adjusting for our top GWAS SNP but these were considered to be of marginal value.

AB - OBJECTIVE: To identify additional genetic variants beyond those observed in a previous genome-wide association study (GWAS) in women treated on the MA.27 clinical trial in which women were randomized to 5 years of adjuvant therapy with anastrozole or exemestane. PATIENTS AND METHODS: We performed a matched case-control study in 234 women who had a recurrence of breast cancer (cases) and 649 women who had not (controls). The analysis was restricted to White women with an estrogen receptor-positive breast cancer. Multiplex PCR-based targeted deep sequencing was performed of the MIR2052HG region on chromosome 8 between positions 75.4 and 75.7, a span of 300 kb, in an attempt to identify additional functional single nucleotide polymorphisms (SNPs). RESULTS: A total of 4677 unique variants were identified that had not been identified in the previous GWAS. Clinical Annotation of Variants analysis revealed 10 variants, including eight SNPs and two insertion-deletion mutations with moderate or high impact. However, none of the common and variant regions was significant after adjustment for the most significant SNP (rs13260300) identified in our previous GWAS. We performed haplotype analysis that revealed two regions in which the haplotypes lost significance when adjusted for this prior GWAS SNP and one region with two significant haplotypes (P = 0.046 and 0.031) after adjusting for the GWAS SNP. CONCLUSION: We were unable to identify common or rare variant regions that added value to the findings from our previous GWAS. We did find two haplotypes that were significant after adjusting for our top GWAS SNP but these were considered to be of marginal value.

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