Detection of Tumor DNA in Plasma Using Whole Genome Amplification

Recent advances and application of whole genome amplification in molecular diagnosis and medicine

Whole genome amplification (WGA) is a technology for non-selective amplification of the whole genome sequence, first appearing in 1992. Its primary purpose is to amplify and reflect the whole genome of trace tissues and single cells without sequence bias and to provide sufficient DNA template for subsequent multigene and multilocus analysis, along with comprehensive genome research. WGA provides a method to obtain a large amount of genetic information from a small amount of DNA and provides a valuable tool for preserving limited samples in molecular biology. WGA technology is especially suitable for forensic identification and genetic disease research, along with new technologies such as next-generation sequencing (NGS). In addition, WGA is also widely used in single-cell sequencing. Due to the small amount of DNA in a single cell, it is often unable to meet the amount of samples needed for sequencing, so WGA is generally used to achieve the amplification of trace samples. This paper reviews WGA methods based on different principles, summarizes both amplification principle and amplification quality, and discusses the application prospects and challenges of WGA technology in molecular diagnosis and medicine.

Increased Plasma Circulating Cell-Free DNA Could Be a Potential Marker for Oral Cancer

Background: Oral squamous cell carcinoma (OSCC) is a disease that affects patients worldwide. DNA of dead cells is released into the blood stream and may be isolated from plasma or serum samples. This DNA is termed cell-free DNA (cfDNA). cfDNA is increased in several types of malignancies. We investigated if there was a correlation between cfDNA levels and the progression of OSCC. Methods: Using quantitative spectrometry, we measured plasma cfDNA in 121 patients with OSCC and 50 matched controls. Mann Whitney and Wilcoxon tests were used to compare differences among various clinical variants. Receiver operating characteristic (ROC) analysis was used to obtain levels suitable for the separation of the clinical subsets. Kaplan-Meier analysis was used to assess correlation with survival. Results: Plasma cfDNA was significantly elevated in patients with OSCC relative to controls. Plasma cfDNA levels correlated with larger tumor size, cervical lymph node metastasis and late stage. Higher plasma cfDNA levels were associated with a poor prognosis of OSCC, which is a new finding. Conclusion: Plasma cfDNA could serve as a novel and easily accessible biomarker in OSCC, providing diagnostic and prognostic value.

Increase of microRNA miR-31 level in plasma could be a potential marker of oral cancer

BACKGROUNDS

Oral squamous cell carcinoma (OSCC) is a worldwide disease. MicroRNAs are endogenously expressed non-coding RNAs that have important biological and pathological functions. miR-31 was found markedly up-regulated in OSCC and several other malignancies. However, miR-31 expression was also down-regulated in the metastasis process of breast carcinoma.

MATERIALS AND METHODS

Using quantitative RT-PCR analysis, we identified plasma miR-31 in OSCC patients (n = 43) and case controlled individuals (n = 21). Nine OSCC patients saliva were also analyzed. The Mann-Whitney test and Wilcoxon matched pairs test were used to compare the differences among the various clinical variants.

RESULTS

miR-31 in plasma was significantly elevated in OSCC patients relative to age and sex-matched control individuals. This marker yielded a receiver operating characteristic curve area of 0.82 and an accuracy of 0.72 defined by leave-one-out cross-validation. In addition, the plasma miR-31 in patients was remarkably reduced after tumor resection suggesting that this marker is tumor associated. Our preliminary analysis also demonstrated the feasibility of detecting the increase of miR-31 in patient's saliva.

CONCLUSION

This study concluded that plasma miR-31 could be validated a marker of OSCC for diagnostic uses.

Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping

BACKGROUND

Whole genome amplification (WGA) offers new possibilities for genome-wide association studies where limited DNA samples have been collected. This study provides a realistic and high-precision assessment of WGA DNA genotyping performance from 20-year old archived serum samples using the Affymetrix Genome-Wide Human SNP Array 6.0 (SNP6.0) platform.

RESULTS

Whole-genome amplified (WGA) DNA samples from 45 archived serum replicates and 5 fresh sera paired with non-amplified genomic DNA were genotyped in duplicate. All genotyped samples passed the imposed QC thresholds for quantity and quality. In general, WGA serum DNA samples produced low call rates (45.00 +/- 2.69%), although reproducibility for successfully called markers was favorable (concordance = 95.61 +/- 4.39%). Heterozygote dropouts explained the majority (>85% in technical replicates, 50% in paired genomic/serum samples) of discordant results. Genotyping performance on WGA serum DNA samples was improved by implementation of Corrected Robust Linear Model with Maximum Likelihood Classification (CRLMM) algorithm but at the loss of many samples which failed to pass its quality threshold. Poor genotype clustering was evident in the samples that failed the CRLMM confidence threshold.

CONCLUSIONS

We conclude that while it is possible to extract genomic DNA and subsequently perform whole-genome amplification from archived serum samples, WGA serum DNA did not perform well and appeared unsuitable for high-resolution genotyping on these arrays.

Loss of heterozygosity (LOH) on chromosomes 2q, 3p and 21q in Indian oral squamous cell carcinoma

Around the world, 200,000 people a year are affected by oral cancer, and the incidence of this disease is 10 times higher in India than Japan, mainly due to the custom of chewing tobacco. Loss of heterozygosity (LOH) on the long arm of chromosome 2 (2q), the short arm of chromosome 3 (3p) and the long arm of chromosome 21 (21q) are observed in several human cancers. We identified novel tumor suppressor loci on these regions in primary oral squamous cell carcinomas (OSCCs) in Japanese. However, there has been no detailed analysis of LOH on these chromosomes in Indians. In the present study, we investigated LOH at 2q, 3p and 21q using 9 microsatellite markers in 26 Indian OSCCs. LOH was detected in 25 (96.2%) out of 26 informative samples at one or more of the loci examined. On the basis of the results, two commonly deleted regions were identified and a detailed deletion map was constructed. In the first region, a high frequency of LOH was observed at the D3S1007 locus (53.8%) on 3p25, which is located in the region neighboring the VHL (von Hippel-Lindau) gene. In the second region, LOH was concentrated at the D3S966 locus (50.0%) on 3p21.3, suggesting the presence of a putative tumor suppressor gene (TSG) associated with OSCCs. These results strongly suggest that there are at least two candidate TSGs located on chromosome 3p, and that alteration in them is associated with the tumorigenesis of OSCCs.