Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20th, 31st, and 81sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68th, 79th, and 95th haplotypes), one was predominant in the South and Southwest China regions (the 18th haplotype), one was relatively common in the Northeast and North China regions (the 94th haplotype), and one was common in the Northeast, North and Northwest China (the 40th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis studies.

/pdf/high-resolution-analyses-of-human-leukocyte-antigens-allele-4jqf1dqmps.pdf

High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program

We present the first accelerated implementation of BWA-MEM, a popular genome sequence alignment algorithm widely used in next generation sequencing genomics pipelines. The Smith-Waterman-like sequence alignment kernel requires a significant portion of overall execution time. We propose and evaluate a number of FPGA-based systolic array architectures, presenting optimizations generally applicable to variable length Smith-Waterman execution. Our kernel implementation is up to 3× faster, compared to software-only execution. This translates into an overall application speedup of up to 45%, which is 96% of the theoretically maximum achievable speedup when accelerating only this kernel.

/pdf/an-fpga-based-systolic-array-to-accelerate-the-bwa-mem-3lm89kd1ey.pdf

An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm

This invention concerns Chemically-sensitive Field Effect Transistors (ChemFETs) that are preferably fabricated using semiconductor fabrication methods on a semiconductor wafer, and in preferred embodiments, on top of an integrated circuit structure made using semiconductor fabrication methods. The instant ChemFETs typically comprise a conductive source, a conductive drain, and a channel composed of a one-dimensional (1D) or two-dimensional (2D) transistor nanomaterial, which channel extends from the source to the drain and is fabricated using semiconductor fabrication techniques on top of a wafer. The ChemFET also includes a gate, often the gate voltage is provided through a fluid or solution proximate the ChemFET. Such ChemFETs, preferably configured in independently addressable arrays, may be employed to detect a presence and/or concentration changes of various analyte types in chemical and/or biological samples, including nucleic acid hybridization and/or sequencing reactions.

Chemically-sensitive field effect transistors, systems, and methods for manufacturing and using the same

Non-invasive prenatal testing (NIPT) using maternal plasma cell free DNA has already reshaped the existing prenatal care system for pregnancies screened for common chromosomal aneuploidies On the other hand, much progress has been made in developing NIPT for monogenic diseases Thalassemia served as a disease model to develop strategies for NIPT of monogenic traits One approach focuses on the detection or exclusion of paternally inherited fetal mutations that are absent from the mother's genome The assessment of maternally inherited mutations in maternal plasma requires the use of highly sensitive DNA quantification techniques The relative mutation dosage (RMD) or the relative haplotype dosage (RHDO) approach provides a powerful tool to elucidate the fetal mutational status even in populations with lower genetic diversity, where the parents share the same mutation With expected decrease in sequencing costs, NIPT for monogenic diseases is becoming an affordable option in prenatal care

Non-invasive prenatal diagnosis of thalassemias using maternal plasma cell free DNA

Provided herein are devices, systems, and methods of employing the same for the performance of bioinformatics analysis. The apparatuses and methods of the disclosure are directed in part to large scale graphene FET sensors, arrays, and integrated circuits employing the same for analyte measurements. The present GFET sensors, arrays, and integrated circuits may be fabricated using conventional CMOS processing techniques based on improved GFET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense GFET sensor based arrays. Improved fabrication techniques employing graphene as a reaction layer provide for rapid data acquisition from small sensors to large and dense arrays of sensors. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes, including DNA hybridization and/or sequencing reactions. Accordingly, GFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis within a gated reaction chamber of the GFET based sensor.

Graphene fet devices, systems, and methods of using the same for sequencing nucleic acids

The invention discloses a CNV analysis method for chromosomes of single-cell and detection device. A CNV analysis method for chromosomes of a single-cell and a detection device, the CNV analysis method for chromosomes of a single-cell comprising the following steps: a first step of extracting effective data; a second step of performing sequence alignment on the extracted effective data then determining whether a Y chromosome is present; a third step of dividing the sequences having undergone sequence alignment into windows then performing GC-content correction; a fourth step of performing breakpoint screening on the data having undergone GC-content correction; a fifth step of filtering the data having undergone breakpoint screening for data satisfying a determining condition and performing visualisation.

CNV analysis method for chromosomes of single-cell and detection device

A PF rapid database construction method and an application therefor. The PF rapid database construction method comprises the following steps: a first step of fragmenting genomic DNA so as to obtain DNA fragments; a second step of performing end repairing on the DNA fragments; a third step of adding P1 and Barcode X adapters at the ends of the DNA fragments having undergone end repairing; a fourth step of performing library mixing according to the required yield of each library; a fifth step of performing nick translation on the mixed libraries; a sixth step of performing quality testing on the product having undergone nick translation.

PF rapid database construction method and application therefor

The present invention provides a method for determining the biological age of an individual to be detected and the use thereof, wherein the method comprises the following steps: according to the above-mentioned method for determining the biological indicator sets for the biological age prediction of population samples, determining various biological indicator sets for biological age prediction ofthe individual to be detected of the population samples classified by gender and age; based on the biological indicator sets for biological age prediction classified by gender and age corresponding tothe individual to be detected, calculating the preliminary estimated value BAEC of the biological age of the individual to be detected; and by taking the age distribution data of samples of differentpopulations as the reference, carrying out maximum posterior probability calculation processing to the preliminary estimated value BAEC of the biological age so as to determine the predicted biological age BA of the individual to be detected.

Method for determining population sample biological indicator set and predicting biological age and use thereof

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CNV analysis method for chromosomes of single-cell and detection device

PF rapid database construction method and application therefor

Method for determining population sample biological indicator set and predicting biological age and use thereof