Abstract P2-03-10: Comprehensive somatic SNV and CNV profiling for triple-negative breast cancer patients by targeted next-generation sequencing
Authors: Yun Taegyun , Lee Byung-Chul , Park Jungsun , Park Dongyoon , Yoo Tae-Kyung , Kim Min Kyoon , Han Wonshik 
Published: May 2015

Introduction: Triple-negative breast cancer is a subtype of breast cancer lacking expression of estrogen receptor, progesterone receptor and HER2/neu protein markers. Despite having the worse prognosis, currently there is no molecular target for this subtype. To discover the clues for therapeutic targets of TNBC, we examined somatic Single Nucleotide Variation (SNV) and Copy Number Variation (CNV) profiling of TNBC patients using targeted next-generation sequencing (NGS).

Methods: A total of 414 breast cancer and normal breast samples were collected at Seoul National University Hospital (SNUH) from 1995 to 2013. By sample condition, 94 samples were frozen tissues (47 tumor-normal matched pair), and 320 samples were formalin-fixed and paraffin-embedded (FFPE) tissues (155 tumor-normal matched pair; Tumor 164, Normal 156). Genomic DNA was extracted from samples and target enrichment was done by using Agilent SureSelect Human Kinome Panel (612 genes including over 500 kinases). The paired-end libraries were constructed and sequenced on Illumina HiSeq 2000 instrument with average 250x depth coverage. Generated sequence reads were aligned to human genome hg19 with bwa algorithm, and somatic SNV and CNV were identified using VarScan2 algorithm. To confirm the existence of identified somatic SNV and CNV, we carried out SNP microarray experiment (Illumina Human Omni5 Exome microarray) for 46 pairs of frozen tissue samples. There were 18,720 SNP probes in SNP microarray covering target region of kinome panel. If the same SNV and CNV were detected in both NGS and microarray data, we considered them validated.

Results: In 46 paired frozen samples, 610 somatic SNVs were detected. The most frequent and non-synonymous mutations were in PIK3CA (8.6%), BMPR1A (4.3%), FES (4.3%), TP53 (4.3%), ROCK1 (4.3%), PAK2 (4.3%), CDK18 (4.3%), OBSCN (4.3%), LRRK1 (4.3%), CDC6 (4.3%), PIKFYVE (4.3%), and FGFR3 (4.3%). Chromosomal aberration was detected in chromosome 1 (10 samples) and chromosome 8 (11 samples). 242 somatic CNV were found in 157 genes in 46 patients, but 99 gene amplifications showed only single occurrence. In other words, TNBC sample displayed highly heterogeneous CNV profile. However, we detected two frequently amplified genes; PKHD1L1 (13%) and NRBP2 (10.9%). Further analysis on NGS data of 155 pairs of FFPE samples is in process to validate the results.

Conclusion: We investigated comprehensive somatic mutation profile in matched pair TNBC samples. Although these samples showed highly heterogeneous mutation profile, it’s possible to detect some interesting SNV and CNV with over 4% frequency. Further analysis may illuminate clinical meaning of those alterations.

Citation Format: Taegyun Yun, Byung-Chul Lee, Jungsun Park, Dongyoon Park, Tae-Kyung Yoo, Min Kyoon Kim, Wonshik Han. Comprehensive somatic SNV and CNV profiling for triple-negative breast cancer patients by targeted next-generation sequencing [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-03-10.