Integrated Microfluidic System for Rapid 89-Plex Y-SNP Profiling: Development and Forensic Validation.

Forensic Y-SNP analysis beyond SNaPshot: High-resolution Y-chromosomal haplogrouping from low quality and quantity DNA using Ion AmpliSeq and targeted massively parallel sequencing

Development and validation of a custom panel including 256 Y-SNPs for Chinese Y-chromosomal haplogroups dissection

Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A pilot study on male Chinese Yunnan Zhaoyang Han population

Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis

Genetic insights into the paternal admixture history of Chinese Mongolians via high-resolution customized Y-SNP SNaPshot panels

Uniparental-inherited haploid genetic marker of Y­chromosome single nucleotide polymorphisms (Y-SNP) have the power to provide a deep understanding of the human evolutionary past, forensic pedigree, and bio-geographical ancestry information. Several international cross-continental or regional Y-panels instead of Y-whole sequencing have recently been developed to promote Y-tools in forensic practice. However, panels based on next-generation sequencing (NGS) explicitly developed for Chinese populations are insufficient to represent the Chinese Y-chromosome genetic diversity and complex population structures, especially for Chinese-predominant haplogroup O. We developed and validated a 639-plex panel including 633 Y-SNPs and 6 Y-Insertion/deletions, which covered 573 Y haplogroups on the Y-DNA haplogroup tree. In this panel, subgroups from haplogroup O accounted for 64.4% of total inferable haplogroups. We reported the sequencing metrics of 354 libraries sequenced with this panel, with the average sequencing depth among 226 individuals being 3,741×. We illuminated the high level of concordance, accuracy, reproducibility, and specificity of the 639-plex panel and found that 610 loci were genotyped with as little as 0.03 ng of genomic DNA in the sensitivity test. 94.05% of the 639 loci were detectable in male-female mixed DNA samples with a mix ratio of 1:500. Nearly all of the loci were genotyped correctly when no more than 25 ng/μL tannic acid, 20 ng/μL humic acid, or 37.5 μM hematin was added to the amplification mixture. More than 80% of genotypes were obtained from degraded DNA samples with a degradation index of 11.76. Individuals from the same pedigree shared identical genotypes in 11 male pedigrees. Finally, we presented the complex evolutionary history of 183 northern Chinese Hans and six other Chinese populations, and found multiple founding lineages that contributed to the northern Han Chinese gene pool. The 639-plex panel proved an efficient tool for Chinese paternal studies and forensic applications.

Microfluidics. Big things in narrow channels.

Microfluidic Devices for Molecular Monitoring of Clonotypic IgH VDJ Signatures and the T(4;14) Translocation in Multiple Myeloma.

BackgroundNon-recombining regions of the Y-chromosome recorded the evolutionary traces of male human populations and are inherited haplotype-dependently and male-specifically. Recent whole Y-chromosome sequencing studies have identified previously unrecognized population divergence, expansion and admixture processes, which promotes a better understanding and application of the observed patterns of Y-chromosome genetic diversity.ResultsHere, we developed one highest-resolution Y-chromosome single nucleotide polymorphism (Y-SNP) panel targeted for uniparental genealogy reconstruction and paternal biogeographical ancestry inference, which included 639 phylogenetically informative SNPs. We genotyped these loci in 1033 Chinese male individuals from 33 ethnolinguistically diverse populations and identified 256 terminal Y-chromosomal lineages with frequency ranging from 0.0010 (singleton) to 0.0687. We identified six dominant common founding lineages associated with different ethnolinguistic backgrounds, which included O2a2b1a1a1a1a1a1a1-M6539, O2a1b1a1a1a1a1a1-F17, O2a2b1a1a1a1a1b1a1b-MF15397, O2a2b2a1b1-A16609, O1b1a1a1a1b2a1a1-F2517, and O2a2b1a1a1a1a1a1-F155. The AMOVA and nucleotide diversity estimates revealed considerable differences and high genetic diversity among ethnolinguistically different populations. We constructed one representative phylogenetic tree among 33 studied populations based on the haplogroup frequency spectrum and sequence variations. Clustering patterns in principal component analysis and multidimensional scaling results showed a genetic differentiation between Tai-Kadai-speaking Li, Mongolic-speaking Mongolian, and other Sinitic-speaking Han Chinese populations. Phylogenetic topology inferred from the BEAST and Network relationships reconstructed from the popART further showed the founding lineages from culturally/linguistically diverse populations, such as C2a/C2b was dominant in Mongolian people and O1a/O1b was dominant in island Li people. We also identified many lineages shared by more than two ethnolinguistically different populations with a high proportion, suggesting their extensive admixture and migration history.ConclusionsOur findings indicated that our developed high-resolution Y-SNP panel included major dominant Y-lineages of Chinese populations from different ethnic groups and geographical regions, which can be used as the primary and powerful tool for forensic practice. We should emphasize the necessity and importance of whole sequencing of more ethnolinguistically different populations, which can help identify more unrecognized population-specific variations for the promotion of Y-chromosome-based forensic applications.

Limitations and Practical Procedure in BclII-Ig Heavy Chain Gene Rearrangement Real-Time Quantitative Polymerase Chain Reaction

Microfluidic Chips for Detecting the t(4;14) Translocation and Monitoring Disease during Treatment Using Reverse Transcriptase-Polymerase Chain Reaction Analysis of IgH-MMSET Hybrid Transcripts

The previously established 38-plex InDel system was optimized and its performance was validated according to the Scientific Working Group on DNA Analysis Method (SWGDAM) application guidelines. The ancestry inference accuracy of individuals from East Asian, European, African and mixed populations was verified. DNA standard sample 9947A was used as the template to establish the optimal amplification conditions by adjusting primer balance, Mg2+ final concentration and optimizing PCR thermal cycle parameters and amplification volume. The allelic dropout, nonspecific amplification and whether the origin of the inferred samples matched the known information were compared to evaluate the performance of this system. The optimal dosage of this system was 0.125-2 ng DNA template. The results of InDel typing were accurate, the amplification equilibrium was good, and the species specificity was good. This system showed certain tolerance to DNA samples including the inhibitor such as hemoglobin (≤80 μmol/L), indigo (≤40 mmol/L), calcium ion (≤1.0 mmol/L), and humic acid (≤90 ng/μL). The system enabled the direct amplification of DNA from saliva and blood on filter paper, and the results of ethnic inference were accurate. The system successfully detected the mixed DNA sample from two individuals. The test results of the system for common biological materials in practical cases were accurate. The results of the 38-plex InDel system are accurate and reliable, and the performance of the system meets the requirement of the SWGDAM guidelines. This system can accurately differentiate the ancestry origins of individuals from African, European, East Asian, and Eurasian populations and can be implemented in forensic practice.

The 3500xL Genetic Analyzer will be used for short tandem repeat (STR) analysis because 3130xl Genetic Analyzer has been discontinued. A validation study was performed for the 3500xL to carry out STR analysis of reference samples with Identifiler® Kit. Sensitivity test was performed with 0.125 ng, 0.5 ng, 1 ng and 3 ng DNA as PCR template. All alleles were detected with 0.5 ng, 1 ng and 3 ng DNA input. Any off scale data and noise over 175 RFU that is threshold value of 3500xL recommended by the manufacturer were not observed from 0.5 ng of input DNA. Thus the optimum input DNA for PCR template was 0.5 ng. We also examined Intra-color peak height ratio and heterozygote peak height ratio at 0.5 ng of template DNA. These results obtained by 3500xL showed similar validations with 310 and 3130xl previously reported. Spectral pull-up was examined by inspections of 240 injections data about each 0.5 ng, 1 ng and 3 ng DNA samples in the sensitivity study with a threshold value of 50 RFU. 1,011, 3,210, and 7,056 pull-up peaks were observed in 0.5 ng, 1 ng, and 3 ng, respectively. It was possible to remove all pull-up peaks using a global cut-off filter of 20%. We compared the profiles generated by the 3500xL and 3130xl using 84 samples with 0.5 ng DNA as PCR template. Both 3500xL and 3130xl detected peaks of all alleles contained in them. However, 3500xL also detected noise peaks and genotyping success rate were 71.4-88.1%. When the 3500xL run data were re-analyzed using the 20% filter, the genotyping results showed 100% concordance. The 20% filter is useful to obtain STR profiles with Identifiler® kit using 3500xL from reference samples because reference samples yield high-quality DNA and are collected from a single individual.

Microfluidics and Circulating Tumor Cells

This study based on the technique, “Electrowetting on Dielectric (EWOD),” with the micro-heaters designed in EWOD microfluidics system for temperature controlling in biomedical reaction. On this platform, fluorescence magnetic beads (MBs) were used as carriers for single-nucleotide polymorphism (SNP) detection. In human genome, SNPs are responsible for the variations between individuals. The genome of a person comprise specific SNP could result in responsiveness to drug therapies and sensitivity of certain disease. Therefore, SNP is considered as one of the keys to predict the affect in pharmacogenomic medicine. In this study, SNP detection has been demonstrated on this thermal controllable EWOD platform in order to approach the goal of “lab-on-a-chip”.