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Shin G, Greer SU, Hopmans E, Grimes SM, Lee H, Zhao L, Miotke L, Suarez C, Almeda AF, Haraldsdottir S, Ji HP. Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8. Genome Med 2021; 13:145. [PMID: 34488871 PMCID: PMC8420050 DOI: 10.1186/s13073-021-00958-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 08/23/2021] [Indexed: 11/10/2022] Open
Abstract
We developed a sensitive sequencing approach that simultaneously profiles microsatellite instability, chromosomal instability, and subclonal structure in cancer. We assessed diverse repeat motifs across 225 microsatellites on colorectal carcinomas. Our study identified elevated alterations at both selected tetranucleotide and conventional mononucleotide repeats. Many colorectal carcinomas had a mix of genomic instability states that are normally considered exclusive. An MSH3 mutation may have contributed to the mixed states. Increased copy number of chromosome arm 8q was most prevalent among tumors with microsatellite instability, including a case of translocation involving 8q. Subclonal analysis identified co-occurring driver mutations previously known to be exclusive.
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Affiliation(s)
- GiWon Shin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Stephanie U Greer
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Erik Hopmans
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Susan M Grimes
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Lan Zhao
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Laura Miotke
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Carlos Suarez
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | - Alison F Almeda
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Sigurdis Haraldsdottir
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA, 94305-5151, USA. .,Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
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2
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Lau BT, Ji HP. Covalent "Click Chemistry"-Based Attachment of DNA onto Solid Phase Enables Iterative Molecular Analysis. Anal Chem 2019; 91:1706-1710. [PMID: 30652472 DOI: 10.1021/acs.analchem.8b05139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular analysis of DNA samples with limited quantities can be challenging. Repeatedly sequencing the original DNA molecules from a given sample would overcome many issues related to accurate genetic analysis and mitigate issues with processing small amounts of DNA analyte. Moreover, an iterative, replicated analysis of the same DNA molecule has the potential to improve genetic characterization. Herein, we demonstrate that the use of "click"-based attachment of DNA sequencing libraries onto an agarose bead support enables repetitive primer extension assays for specific genomic DNA targets such as gene exons. We validated the performance of this assay for evaluating specific genetic alterations in both normal and cancer reference standard DNA samples. We demonstrate the stability of conjugated DNA libraries and related sequencing results over the course of independent serial assays spanning several months from the same set of samples. Finally, we finally applied this method to DNA derived from a tumor sample and demonstrated improved mutation detection accuracy.
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Affiliation(s)
- Billy T Lau
- Stanford Genome Technology Center , Stanford University , Palo Alto , California 94304 , United States
| | - Hanlee P Ji
- Stanford Genome Technology Center , Stanford University , Palo Alto , California 94304 , United States.,Division of Oncology , Stanford School of Medicine , Stanford , California 94305 , United States
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3
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Pel J, Leung A, Choi WWY, Despotovic M, Ung WL, Shibahara G, Gelinas L, Marziali A. Rapid and highly-specific generation of targeted DNA sequencing libraries enabled by linking capture probes with universal primers. PLoS One 2018; 13:e0208283. [PMID: 30517195 PMCID: PMC6281261 DOI: 10.1371/journal.pone.0208283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/14/2018] [Indexed: 11/18/2022] Open
Abstract
Targeted Next Generation Sequencing (NGS) is being adopted increasingly broadly in many research, commercial and clinical settings. Currently used target capture methods, however, typically require complex and lengthy (sometimes multi-day) workflows that complicates their use in certain applications. In addition, small panels for high sequencing depth applications such as liquid biopsy typically have low on-target rates, resulting in unnecessarily high sequencing cost. We have developed a novel targeted sequencing library preparation method, named Linked Target Capture (LTC), which replaces typical multi-day target capture workflows with a single-day, combined ‘target-capture-PCR’ workflow. This approach uses physically linked capture probes and PCR primers and is expected to work with panel sizes from 100 bp to >10 Mbp. It reduces the time and complexity of the capture workflow, eliminates long hybridization and wash steps and enables rapid library construction and target capture. High on-target read fractions are achievable due to repeated sequence selection in the target-capture-PCR step, thus lowering sequencing cost. We have demonstrated this technology on sample types including cell-free DNA (cfDNA) and formalin-fixed, paraffin-embedded (FFPE) derived DNA, capturing a 35-gene pan-cancer panel, and therein detecting single nucleotide variants, copy number variants, insertions, deletions and gene fusions. With the integration of unique molecular identifiers (UMIs), variants as low as 0.25% abundance were detected, limited by input mass and sequencing depth. Additionally, sequencing libraries were prepared in less than eight hours from extracted DNA to loaded sequencer, demonstrating that LTC holds promise as a broadly applicable tool for rapid, cost-effective and high performance targeted sequencing.
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Affiliation(s)
- Joel Pel
- Boreal Genomics Inc, Vancouver, British Columbia, Canada
| | - Amy Leung
- Boreal Genomics Inc, Vancouver, British Columbia, Canada
| | | | | | - W. Lloyd Ung
- Boreal Genomics Inc, Vancouver, British Columbia, Canada
| | | | - Laura Gelinas
- Boreal Genomics Inc, Vancouver, British Columbia, Canada
| | - Andre Marziali
- Boreal Genomics Inc, Vancouver, British Columbia, Canada
- University of British Columbia, Department of Physics and Astronomy, Vancouver, British Columbia, Canada
- * E-mail:
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4
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A robust targeted sequencing approach for low input and variable quality DNA from clinical samples. NPJ Genom Med 2018; 3:2. [PMID: 29354287 PMCID: PMC5768874 DOI: 10.1038/s41525-017-0041-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/27/2017] [Accepted: 12/05/2017] [Indexed: 02/07/2023] Open
Abstract
Next-generation deep sequencing of gene panels is being adopted as a diagnostic test to identify actionable mutations in cancer patient samples. However, clinical samples, such as formalin-fixed, paraffin-embedded specimens, frequently provide low quantities of degraded, poor quality DNA. To overcome these issues, many sequencing assays rely on extensive PCR amplification leading to an accumulation of bias and artifacts. Thus, there is a need for a targeted sequencing assay that performs well with DNA of low quality and quantity without relying on extensive PCR amplification. We evaluate the performance of a targeted sequencing assay based on Oligonucleotide Selective Sequencing, which permits the enrichment of genes and regions of interest and the identification of sequence variants from low amounts of damaged DNA. This assay utilizes a repair process adapted to clinical FFPE samples, followed by adaptor ligation to single stranded DNA and a primer-based capture technique. Our approach generates sequence libraries of high fidelity with reduced reliance on extensive PCR amplification—this facilitates the accurate assessment of copy number alterations in addition to delivering accurate single nucleotide variant and insertion/deletion detection. We apply this method to capture and sequence the exons of a panel of 130 cancer-related genes, from which we obtain high read coverage uniformity across the targeted regions at starting input DNA amounts as low as 10 ng per sample. We demonstrate the performance using a series of reference DNA samples, and by identifying sequence variants in DNA from matched clinical samples originating from different tissue types. A new DNA sequencing technology enables comprehensive genetic analyses of poor-quality tumor samples. Hanlee Ji from Stanford University in California, USA, together with colleagues from a company he cofounded called TOMA Biosciences, tested the performance of a targeted sequencing assay known as oligonucleotide-selective sequencing (OS-Seq). They used the “in-solution” version of OS-Seq, which involves a pre-processing step to remove any damaged DNA and then sequences target regions of the genome to look for duplications, insertions or deletions of DNA segments. Using archival specimens (which often contain low quantities of degraded DNA) from patients with lung and colorectal cancer, the researchers showed they could detect sequence variants in a panel of 130 cancer-related genes. The findings suggest the OS-Seq assay could help inform treatment decisions for cancer patients, even with clinical specimens of low quality.
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Single-Color Digital PCR Provides High-Performance Detection of Cancer Mutations from Circulating DNA. J Mol Diagn 2017; 19:697-710. [PMID: 28818432 PMCID: PMC6593258 DOI: 10.1016/j.jmoldx.2017.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 02/02/2023] Open
Abstract
We describe a single-color digital PCR assay that detects and quantifies cancer mutations directly from circulating DNA collected from the plasma of cancer patients. This approach relies on a double-stranded DNA intercalator dye and paired allele-specific DNA primer sets to determine an absolute count of both the mutation and wild-type–bearing DNA molecules present in the sample. The cell-free DNA assay uses an input of 1 ng of nonamplified DNA, approximately 300 genome equivalents, and has a molecular limit of detection of three mutation DNA genome-equivalent molecules per assay reaction. When using more genome equivalents as input, we demonstrated a sensitivity of 0.10% for detecting the BRAF V600E and KRAS G12D mutations. We developed several mutation assays specific to the cancer driver mutations of patients' tumors and detected these same mutations directly from the nonamplified, circulating cell-free DNA. This rapid and high-performance digital PCR assay can be configured to detect specific cancer mutations unique to an individual cancer, making it a potentially valuable method for patient-specific longitudinal monitoring.
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Shin G, Grimes SM, Lee H, Lau BT, Xia LC, Ji HP. CRISPR-Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis. Nat Commun 2017; 8:14291. [PMID: 28169275 PMCID: PMC5309709 DOI: 10.1038/ncomms14291] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 12/15/2016] [Indexed: 11/09/2022] Open
Abstract
Microsatellites are multi-allelic and composed of short tandem repeats (STRs) with individual motifs composed of mononucleotides, dinucleotides or higher including hexamers. Next-generation sequencing approaches and other STR assays rely on a limited number of PCR amplicons, typically in the tens. Here, we demonstrate STR-Seq, a next-generation sequencing technology that analyses over 2,000 STRs in parallel, and provides the accurate genotyping of microsatellites. STR-Seq employs in vitro CRISPR-Cas9-targeted fragmentation to produce specific DNA molecules covering the complete microsatellite sequence. Amplification-free library preparation provides single molecule sequences without unique molecular barcodes. STR-selective primers enable massively parallel, targeted sequencing of large STR sets. Overall, STR-Seq has higher throughput, improved accuracy and provides a greater number of informative haplotypes compared with other microsatellite analysis approaches. With these new features, STR-Seq can identify a 0.1% minor genome fraction in a DNA mixture composed of different, unrelated samples.
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Affiliation(s)
- GiWon Shin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, CCSR 1115, 269 Campus Drive, Stanford, California 94305, USA
| | - Susan M Grimes
- Stanford Genome Technology Center, Stanford University, 3165 Porter Drive, Palo Alto, California 94304, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, CCSR 1115, 269 Campus Drive, Stanford, California 94305, USA
| | - Billy T Lau
- Stanford Genome Technology Center, Stanford University, 3165 Porter Drive, Palo Alto, California 94304, USA
| | - Li C Xia
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, CCSR 1115, 269 Campus Drive, Stanford, California 94305, USA
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, CCSR 1115, 269 Campus Drive, Stanford, California 94305, USA.,Stanford Genome Technology Center, Stanford University, 3165 Porter Drive, Palo Alto, California 94304, USA
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Xia LC, Sakshuwong S, Hopmans ES, Bell JM, Grimes SM, Siegmund DO, Ji HP, Zhang NR. A genome-wide approach for detecting novel insertion-deletion variants of mid-range size. Nucleic Acids Res 2016; 44:e126. [PMID: 27325742 PMCID: PMC5009736 DOI: 10.1093/nar/gkw481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 05/15/2016] [Indexed: 11/14/2022] Open
Abstract
We present SWAN, a statistical framework for robust detection of genomic structural variants in next-generation sequencing data and an analysis of mid-range size insertion and deletions (<10 Kb) for whole genome analysis and DNA mixtures. To identify these mid-range size events, SWAN collectively uses information from read-pair, read-depth and one end mapped reads through statistical likelihoods based on Poisson field models. SWAN also uses soft-clip/split read remapping to supplement the likelihood analysis and determine variant boundaries. The accuracy of SWAN is demonstrated by in silico spike-ins and by identification of known variants in the NA12878 genome. We used SWAN to identify a series of novel set of mid-range insertion/deletion detection that were confirmed by targeted deep re-sequencing. An R package implementation of SWAN is open source and freely available.
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Affiliation(s)
- Li C Xia
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA Department of Statistics, the Wharton School, University of Pennsylvania, Philadelphia, PA 18014, USA
| | - Sukolsak Sakshuwong
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Erik S Hopmans
- Stanford Genome Technology Centre, Stanford University, Palo Alto, CA 94304, USA
| | - John M Bell
- Stanford Genome Technology Centre, Stanford University, Palo Alto, CA 94304, USA
| | - Susan M Grimes
- Stanford Genome Technology Centre, Stanford University, Palo Alto, CA 94304, USA
| | - David O Siegmund
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA Stanford Genome Technology Centre, Stanford University, Palo Alto, CA 94304, USA
| | - Nancy R Zhang
- Department of Statistics, the Wharton School, University of Pennsylvania, Philadelphia, PA 18014, USA
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8
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Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. Nat Biotechnol 2016; 34:303-11. [PMID: 26829319 PMCID: PMC4786454 DOI: 10.1038/nbt.3432] [Citation(s) in RCA: 438] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 11/12/2015] [Indexed: 01/13/2023]
Abstract
Haplotyping of human chromosomes is a prerequisite for cataloguing the full repertoire of genetic variation. We present a microfluidics-based, linked-read sequencing technology that can phase and haplotype germline and cancer genomes using nanograms of input DNA. This high-throughput platform prepares barcoded libraries for short-read sequencing and computationally reconstructs long-range haplotype and structural variant information. We generate haplotype blocks in a nuclear trio that are concordant with expected inheritance patterns and phase a set of structural variants. We also resolve the structure of the EML4-ALK gene fusion in the NCI-H2228 cancer cell line using phased exome sequencing. Finally, we assign genetic aberrations to specific megabase-scale haplotypes generated from whole-genome sequencing of a primary colorectal adenocarcinoma. This approach resolves haplotype information using up to 100 times less genomic DNA than some methods and enables the accurate detection of structural variants.
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9
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Miotke L, Maity A, Ji H, Brewer J, Astakhova K. Enzyme-Free Detection of Mutations in Cancer DNA Using Synthetic Oligonucleotide Probes and Fluorescence Microscopy. PLoS One 2015; 10:e0136720. [PMID: 26312489 PMCID: PMC4552304 DOI: 10.1371/journal.pone.0136720] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/07/2015] [Indexed: 11/19/2022] Open
Abstract
Background Rapid reliable diagnostics of DNA mutations are highly desirable in research and clinical assays. Current development in this field goes simultaneously in two directions: 1) high-throughput methods, and 2) portable assays. Non-enzymatic approaches are attractive for both types of methods since they would allow rapid and relatively inexpensive detection of nucleic acids. Modern fluorescence microscopy is having a huge impact on detection of biomolecules at previously unachievable resolution. However, no straightforward methods to detect DNA in a non-enzymatic way using fluorescence microscopy and nucleic acid analogues have been proposed so far. Methods and Results Here we report a novel enzyme-free approach to efficiently detect cancer mutations. This assay includes gene-specific target enrichment followed by annealing to oligonucleotides containing locked nucleic acids (LNAs) and finally, detection by fluorescence microscopy. The LNA containing probes display high binding affinity and specificity to DNA containing mutations, which allows for the detection of mutation abundance with an intercalating EvaGreen dye. We used a second probe, which increases the overall number of base pairs in order to produce a higher fluorescence signal by incorporating more dye molecules. Indeed we show here that using EvaGreen dye and LNA probes, genomic DNA containing BRAF V600E mutation could be detected by fluorescence microscopy at low femtomolar concentrations. Notably, this was at least 1000-fold above the potential detection limit. Conclusion Overall, the novel assay we describe could become a new approach to rapid, reliable and enzyme-free diagnostics of cancer or other associated DNA targets. Importantly, stoichiometry of wild type and mutant targets is conserved in our assay, which allows for an accurate estimation of mutant abundance when the detection limit requirement is met. Using fluorescence microscopy, this approach presents the opportunity to detect DNA at single-molecule resolution and directly in the biological sample of choice.
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Affiliation(s)
- Laura Miotke
- The Division of Oncology, Stanford School of Medicine, Stanford University, Stanford, California, United States of America
| | - Arindam Maity
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
- Dr B C Roy College of Pharmacy and AHS, Durgapur, West Bengal, India
| | - Hanlee Ji
- The Division of Oncology, Stanford School of Medicine, Stanford University, Stanford, California, United States of America
| | - Jonathan Brewer
- Memphys Center for Biomembrane Physics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Kira Astakhova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
- * E-mail:
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