scholarly journals Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing

2013 ◽  
Vol 59 (1) ◽  
pp. 211-224 ◽  
Author(s):  
KC Allen Chan ◽  
Peiyong Jiang ◽  
Yama WL Zheng ◽  
Gary JW Liao ◽  
Hao Sun ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Cancer Patients ◽  
Copy Number ◽  
Massively Parallel Sequencing ◽  
Point Mutations ◽  
Cancer Genome ◽  
Massively Parallel ◽  
Plasma Dna ◽  
Parallel Sequencing ◽  
Copy Number Aberrations

BACKGROUND Tumor-derived DNA can be found in the plasma of cancer patients. In this study, we explored the use of shotgun massively parallel sequencing (MPS) of plasma DNA from cancer patients to scan a cancer genome noninvasively. METHODS Four hepatocellular carcinoma patients and a patient with synchronous breast and ovarian cancers were recruited. DNA was extracted from the tumor tissues, and the preoperative and postoperative plasma samples of these patients were analyzed with shotgun MPS. RESULTS We achieved the genomewide profiling of copy number aberrations and point mutations in the plasma of the cancer patients. By detecting and quantifying the genomewide aggregated allelic loss and point mutations, we determined the fractional concentrations of tumor-derived DNA in plasma and correlated these values with tumor size and surgical treatment. We also demonstrated the potential utility of this approach for the analysis of complex oncologic scenarios by studying the patient with 2 synchronous cancers. Through the use of multiregional sequencing of tumoral tissues and shotgun sequencing of plasma DNA, we have shown that plasma DNA sequencing is a valuable approach for studying tumoral heterogeneity. CONCLUSIONS Shotgun DNA sequencing of plasma is a potentially powerful tool for cancer detection, monitoring, and research.

scholarly journals Noninvasive Prenatal Diagnosis of Monogenic Diseases by Targeted Massively Parallel Sequencing of Maternal Plasma: Application to β-Thalassemia

2012 ◽  
Vol 58 (10) ◽  
pp. 1467-1475 ◽  
Author(s):  
Kwan-Wood G Lam ◽  
Peiyong Jiang ◽  
Gary J W Liao ◽  
K C Allen Chan ◽  
Tak Y Leung ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Massively Parallel Sequencing ◽  
Globin Gene ◽  
Maternal Plasma ◽  
Massively Parallel ◽  
Sequencing Data ◽  
Plasma Dna ◽  
Parallel Sequencing ◽  
Noninvasive Prenatal Diagnosis ◽  
Monogenic Diseases

Abstract BACKGROUND A genomewide genetic and mutational profile of a fetus was recently determined via deep sequencing of maternal plasma DNA. This technology could have important applications for noninvasive prenatal diagnosis (NIPD) of many monogenic diseases. Relative haplotype dosage (RHDO) analysis, a core step of this procedure, would allow one to elucidate the maternally inherited half of the fetal genome. For clinical applications, the cost and complexity of data analysis might be reduced via targeted application of this approach to selected genomic regions containing disease-causing genes. There is thus a need to explore the feasibility of performing RHDO analysis in a targeted manner. METHODS We performed target enrichment by using solution-phase hybridization followed by massively parallel sequencing of the β-globin gene region in 2 families undergoing prenatal diagnosis for β-thalassemia. We used digital PCR strategies to physically deduce parental haplotypes. Finally, we performed RHDO analysis with target-enriched sequencing data and parental haplotypes to reveal the β-thalassemic status for the fetuses. RESULTS A mean sequencing depth of 206-fold was achieved in the β-globin gene region by targeted sequencing of maternal plasma DNA. RHDO analysis was successful for the sequencing data obtained from the target-enriched samples, including a region in one of the families in which the parents had similar haplotype structures. Data analysis revealed that both fetuses were heterozygous carriers of β-thalassemia. CONCLUSIONS Targeted sequencing of maternal plasma DNA for NIPD of monogenic diseases is feasible.

scholarly journals Clinical Massively Parallel Sequencing

2019 ◽  
Vol 66 (1) ◽  
pp. 77-88
Author(s):  
Ge Gao ◽  
David I Smith
Keyword(s):  
Clinical Practice ◽  
Dna Sequencing ◽  
Genome Sequencing ◽  
First Generation ◽  
Second Generation ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Near Term ◽  
Gene Panels

Abstract BACKGROUND The newest advances in DNA sequencing are based on technologies that perform massively parallel sequencing (MPS). Since 2006, the output from MPS platforms has increased from 20 Mb to >7 Tb. First-generation MPS platforms amplify individual DNA molecules to multiple copies and then interrogate the sequence of those molecules. Second-generation MPS analyzes single unamplified molecules to generate much longer sequence reads but with less output than first-generation MPS and lower first-pass accuracy. With MPS technologies, it is now possible to analyze genomes, exomes, a defined subset of genes, transcriptomes, and even methylation across the genome. These technologies have and will continue to completely transform the clinical practice. CONTENT The major first- and second-generation MPS platforms and how they are used in clinical practice are discussed. SUMMARY The ability to sequence terabases of DNA per run on an MPS platform will dramatically change how DNA sequencing is used in clinical practice. Currently, MPS of targeted gene panels is the most common use of this technology clinically, but as the cost for genome sequencing inches downward to $100, this may soon become the method of choice (with the caveat that, at least in the near term, clinical-grade genome sequencing with interpretation may cost much more than $100). Other uses of this technology include sequencing of a mixture of bacterial and viral species (metagenomics), as well as the characterization of methylation across the genome.

scholarly journals Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population

2017 ◽  
Vol 32 (4) ◽  
pp. 587 ◽  
Author(s):  
Sohyung Park ◽  
Sohee Cho ◽  
Hee Jin Seo ◽  
Ji Hyun Lee ◽  
Moon-Young Kim ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequencing ◽  
Massively Parallel Sequencing ◽  
Korean Population ◽  
Massively Parallel ◽  
Parallel Sequencing

scholarly journals Maternal Plasma DNA Analysis with Massively Parallel Sequencing by Ligation for Noninvasive Prenatal Diagnosis of Trisomy 21

2010 ◽  
Vol 56 (3) ◽  
pp. 459-463 ◽  
Author(s):  
Rossa WK Chiu ◽  
Hao Sun ◽  
Ranjit Akolekar ◽  
Christopher Clouser ◽  
Clarence Lee ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Trisomy 21 ◽  
Massively Parallel Sequencing ◽  
Maternal Plasma ◽  
Chromosome 21 ◽  
Massively Parallel ◽  
Plasma Dna ◽  
Parallel Sequencing ◽  
Noninvasive Prenatal Diagnosis ◽  
Sequencing By Synthesis

Abstract Background: Noninvasive prenatal diagnosis of trisomy 21 (T21) has recently been shown to be achievable by massively parallel sequencing of maternal plasma on a sequencing-by-synthesis platform. The quantification of several other human chromosomes, including chromosomes 18 and 13, has been shown to be less precise, however, with quantitative biases related to the chromosomal GC content. Methods: Maternal plasma DNA from 10 euploid and 5 T21 pregnancies was sequenced with a sequencing-by-ligation approach. We calculated the genomic representations (GRs) of sequenced reads from each chromosome and their associated measurement CVs and compared the GRs of chromosome 21 (chr21) for the euploid and T21 pregnancies. Results: We obtained a median of 12 × 106 unique reads (21% of the total reads) per sample. The GRs deviated from those expected for some chromosomes but in a manner different from that previously reported for the sequencing-by-synthesis approach. Measurements of the GRs for chromosomes 18 and 13 were less precise than for chr21. z Scores of the GR of chr21 were increased in the T21 pregnancies, compared with the euploid pregnancies. Conclusions: Massively parallel sequencing-by-ligation of maternal plasma DNA was effective in identifying T21 fetuses noninvasively. The quantitative biases observed among the GRs of certain chromosomes were more likely based on analytical factors than biological factors. Further research is needed to enhance the precision for measuring for the representations of chromosomes 18 and 13.

scholarly journals Noninvasive prenatal diagnosis of monogenic disorders based on direct haplotype phasing through targeted linked-read sequencing

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Chao Chen ◽  
Min Chen ◽  
Yaping Zhu ◽  
Lu Jiang ◽  
Jia Li ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Massively Parallel Sequencing ◽  
Effective Means ◽  
Massively Parallel ◽  
Nucleotide Polymorphisms ◽  
Plasma Dna ◽  
Parallel Sequencing ◽  
Monogenic Disorders ◽  
Noninvasive Prenatal Diagnosis ◽  
Hmw Dna

Abstract Background Though massively parallel sequencing has been widely applied to noninvasive prenatal screen for common trisomy, the clinical use of massively parallel sequencing to noninvasive prenatal diagnose monogenic disorders is limited. This study was to develop a method for directly determining paternal haplotypes for noninvasive prenatal diagnosis of monogenic disorders without requiring proband’s samples. Methods The study recruited 40 families at high risk for autosomal recessive diseases. The targeted linked-read sequencing was performed on high molecular weight (HMW) DNA of parents using customized probes designed to capture targeted genes and single-nucleotide polymorphisms (SNPs) distributed within 1Mb flanking region of targeted genes. Plasma DNA from pregnant mothers also underwent targeted sequencing using the same probes to determine fetal haplotypes according to parental haplotypes. The results were further confirmed by invasive prenatal diagnosis. Results Seventy-eight parental haplotypes of targeted gene were successfully determined by targeted linked-read sequencing. The predicted fetal inheritance of variant was correctly deduced in 38 families in which the variants had been confirmed by invasive prenatal diagnosis. Two families were determined to be no-call. Conclusions Targeted linked-read sequencing method demonstrated to be an effective means to phase personal haplotype for noninvasive prenatal diagnosis of monogenic disorders.

scholarly journals Targeted Massively Parallel Sequencing of Maternal Plasma DNA Permits Efficient and Unbiased Detection of Fetal Alleles

2011 ◽  
Vol 57 (1) ◽  
pp. 92-101 ◽  
Author(s):  
Gary JW Liao ◽  
Fiona MF Lun ◽  
Yama WL Zheng ◽  
KC Allen Chan ◽  
Tak Y Leung ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Massively Parallel Sequencing ◽  
Maternal Plasma ◽  
Targeted Sequencing ◽  
Massively Parallel ◽  
Target Enrichment ◽  
Plasma Dna ◽  
Parallel Sequencing ◽  
Fetal Dna ◽  
Genomic Regions

BACKGROUND Massively parallel sequencing has recently been used in noninvasive prenatal diagnosis. The current costs of this technology are still relatively expensive, however, and sample throughput is still relatively low when it is used as a molecular diagnostic tool. Rather than nonselectively sequencing the genome, target enrichment provides a logical approach for more efficient and cost-effective massively parallel sequencing because it increases the proportion of informative data from the targeted region(s). Existing applications of targeted sequencing have mainly been qualitative analyses of genomic DNA. In this study, we investigated its applicability in enriching selected genomic regions from plasma DNA and the quantitative performance of this approach. METHODS DNA was extracted from plasma samples collected from 12 pregnant women carrying female fetuses. The SureSelect Target Enrichment System (Agilent Technologies) was used to enrich for exons on chromosome X. Plasma DNA libraries with and without target enrichment were analyzed by massively parallel sequencing. Genomic DNA samples of the mother and fetus for each case were genotyped by microarray. RESULTS For the regions targeted by the enrichment kit, the mean sequence coverage of the enriched samples was 213-fold higher than that of the nonenriched samples. Maternal and fetal DNA molecules were enriched evenly. After target enrichment, the coverage of fetus-specific alleles within the targeted region increased from 3.5% to 95.9%. CONCLUSIONS Targeted sequencing of maternal plasma DNA permits efficient and unbiased detection of fetal alleles at genomic regions of interest and is a powerful method for measuring the proportion of fetal DNA in a maternal plasma sample.

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