Single Cell Genomics: Whole Genome Sequencing of Single Circulating Tumor Cells Isolated by Applying a Pulsed Laser to Cell‐Capturing Microstructures (Small 37/2019)

Small ◽  
2019 ◽  
Vol 15 (37) ◽  
pp. 1970196 ◽  
Author(s):  
Okju Kim ◽  
Daewon Lee ◽  
Amos Chungwon Lee ◽  
Yongju Lee ◽  
Hyung Jong Bae ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Single Cell ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Genome Sequencing ◽  
Pulsed Laser ◽  
Whole Genome ◽  
Single Cell Genomics

Prevalence and tissue concordance of BRCA2 copy number loss evaluated by single-cell, shallow whole genome sequencing of circulating tumor cells (CTCs) in castration-resistant prostate cancer (CRPC).

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 5531-5531
Author(s):  
Ethan Barnett ◽  
Joseph Schonhoft ◽  
Nikolaus D. Schultz ◽  
Jerry Lee ◽  
Samir Zaidi ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Whole Genome Sequencing ◽  
Single Cell ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Genome Sequencing ◽  
Copy Number ◽  
Cellular Heterogeneity ◽  
Cancer Tissue ◽  
Whole Genome

5531 Background: Genomic studies have shown that up to 25% of prostate cancer tissue specimens harbor alterations in DNA Damage Repair (DDR) genes, which may sensitize the tumor to poly ADP-ribose polymerase inhibitors (PARPi). Trials evaluating PARPi in patients with DDR deficiencies have shown varied response rates and differences regarding which genomic alterations predict for sensitivity to these agents, with the majority of objective responses seen in BRCA2-altered tumors. These results highlight the need to develop biomarker assays which can predict benefit from PARPi therapy. Tissue and cell-free DNA (cfDNA) have been the most utilized sources of tumor material for analysis in this setting, but success rates of obtaining sufficient tumor for analysis from bone are low and detecting tumor-derived copy number variants (CNVs) in cfDNA is challenging. Circulating tumor cells (CTCs) represent an alternate source of genetic information, for which assays are available to isolate and sequence individual cells in a manner that eliminates background noise from stroma and healthy cells, while capturing inter-cellular heterogeneity. Methods: Blood samples, collected from 138 progressing metastatic CRPC patients within 30 days of a pre-treatment biopsy intended for sequencing using MSK-IMPACT, were sent to EPIC Sciences for CTC analysis. Detected CTCs underwent single cell, low pass whole genome sequencing. Prevalence and concordance of BRCA2 copy-loss, regardless of whether single copy or homozygous, was compared in matched tissue and CTC samples. Results: BRCA2 copy-loss was identified in 21% (23/108) and 50% (58/115) of successfully sequenced tissue and CTC samples, respectively. In the 58 patients with CTC-detected BRCA2 loss, BRCA2 loss was detected in 36% (220/565) of the sequenced CTCs, representing a median of 46% (range 4-100%) of CTCs found in each individual sample. When both sequencing assays were successful, BRCA2 loss was detected in CTCs in 84% (16/19) of the tissue-positive cases, whereas tissue sequencing detected BRCA2 loss in 35% (16/46) of CTC-positive cases. Conclusions: Data from this study supports the notion that single-cell CTC sequencing can detect BRCA2 copy-loss at a high frequency, including cases that were negative in tissue, while also characterizing inter-cellular heterogeneity. Further studies will investigate whether CTC BRCA2 copy-loss can predict the likelihood of response to PARPi.

Whole Genome Sequencing of Single Circulating Tumor Cells Isolated by Applying a Pulsed Laser to Cell‐Capturing Microstructures

Small ◽  
2019 ◽  
Vol 15 (37) ◽  
pp. 1902607 ◽  
Author(s):  
Okju Kim ◽  
Daewon Lee ◽  
Amos Chungwon Lee ◽  
Yongju Lee ◽  
Hyung Jong Bae ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Genome Sequencing ◽  
Pulsed Laser ◽  
Whole Genome

Device for whole genome sequencing single circulating tumor cells from whole blood

Lab on a Chip ◽  
2019 ◽  
Vol 19 (19) ◽  
pp. 3168-3178 ◽  
Author(s):  
Ren Li ◽  
Fei Jia ◽  
Weikai Zhang ◽  
Fanghao Shi ◽  
Zhiguo Fang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Genome Sequencing ◽  
Microfluidic Chip ◽  
Whole Blood ◽  
Whole Genome

To sequence single circulating tumor cells (CTCs) from whole blood, a microfluidic chip was developed to perform blood filtering/CTC enrichment/CTC sorting and in situ MDA for whole genome sequencing.

scholarly journals Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer

2017 ◽  
Vol 77 (16) ◽  
pp. 4530-4541 ◽  
Author(s):  
Natali Gulbahce ◽  
Mark Jesus M. Magbanua ◽  
Robert Chin ◽  
Misha R. Agarwal ◽  
Xuhao Luo ◽  
...  
Keyword(s):  
Combination Therapy ◽  
Whole Genome Sequencing ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Genome Sequencing ◽  
Metastatic Cancer ◽  
Whole Genome

scholarly journals Somatic copy number profiling of hepatocellular carcinoma circulating tumor cells.

2018 ◽  
Vol 36 (4_suppl) ◽  
pp. 290-290
Author(s):  
Colin MacDonald Court ◽  
Shuang Hou ◽  
Paul Winograd ◽  
Saeed Sadeghi ◽  
Richard S. Finn ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Whole Genome Sequencing ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Genome Sequencing ◽  
Primary Tumor ◽  
Copy Number ◽  
Whole Genome ◽  
Low Resolution ◽  
Comparison Results

290 Background: Copy number variations (CNVs) have shown prognostic and predictive utility in hepatocellular carcinoma (HCC) but their use from percutaneous biopsies is limited due to HCC’s significant tumor heterogeneity. We investigated the feasibility of obtaining CNV profiles from circulating tumor cells (CTCs) as a liquid biopsy for HCC. Methods: Using a microfluidic HCC-specific CTC assay, CTCs were isolated from 10 patients with HCC and low-resolution (~0.01x) whole genome sequencing performed to establish CNV profiles. Primary tumor, peritumoral liver, and germline DNA was sequenced for comparison. Results: Sequencing of 18 CTC samples (median 4 CTCs/sample) from 10 HCC patients using a low-resolution whole genome sequencing strategy (median 0.88 million reads/sample) revealed frequent copy number changes in previously reported HCC regions such as 8q amplifications and 17p deletions. Analysis of CNV profiles revealed that CTCs share a median of 80% concordance with the primary tumor and that CTCs clustered with their respective primary tumor for 9/10 samples. Sequencing of 7 different CTC samples from a single patient established the reproducibility of the assay. CTCs also demonstrated CNVs not seen in the primary tumor, some with prognostic implications. Conclusions: CNV profiling of HCC-CTCs is feasible and accurately recapitulates CNVs seen in the primary tumor. The use of CTC-derived genetic profiles as clinically relevant surrogates of HCC tumors demonstrates potential and should be explored further. [Table: see text]

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