The Chinese University of Hong Kong is a public research university in Shatin, Hong Kong, formally established in 1963 by a charter granted by the Legislative Council of Hong Kong. It is the territory's second oldest institution of higher learning, and the only collegiate university. The University was originally founded as a federation of three existing colleges, Chung Chi College, New Asia College and United College, the oldest of which was founded in 1949.Today, CUHK is organised into nine constituent colleges and eight academic faculties. Though the original statement in the charter of the University stipulates Chinese as the principal language, English is currently the main language of instruction in most classes, with Cantonese and Mandarin Chinese being retained only by a minority of colleges and academic departments. As of 2013, four Nobel laureates are associated with the University, making it the only tertiary institution in the territory with recipients of the Nobel Prize, Turing Award, Fields Medal and Veblen Prize as faculty in residence. Wikipedia.
Chinese University of Hong Kong | Date: 2017-08-09
A method for analyzing a biological sample of a pregnant female to determine whether at least two fetuses of the pregnant female are dizygotic, the biological sample comprising fetal and maternal DNA, the method comprising: creating a histogram by: for each of a plurality of chromosomal regions: identifying one or more loci in the respective chromosomal region at which a respective first allele and a respective second allele are detected in the biological sample; measuring, at the one or more loci, a first amount of the one or more first alleles and/or a second amount of the one or more second alleles in the biological sample; and obtaining a normalized parameter for the first amount or the second amount; and incrementing counters based on a number of chromosomal regions with specified values for the normalized parameter; identifying chromosomal regions corresponding to loci at which the mother is homozygous and at least one of the fetuses is heterozygous or corresponding to loci at which the mother is heterozygous and at least one of the fetuses is homozygous; fitting a multi-component mixture model to the histogram corresponding to the identified chromosomal regions, the multi-component mixture model including a mixture coefficient for each of a plurality of components; and determining whether at least two of the fetuses are dizygotic using at least two of the mixture coefficients.
Chinese University of Hong Kong | Date: 2017-04-19
Systems, apparatus, and methods are provided for determining aberrations in a biological sample from an organism. Biological samples including cell-free DNA fragments are analyzed to identify imbalances in chromosomal regions, e.g., due to deletions and/or amplifications in a tumor. Multiple loci are used for each chromosomal region. Imbalances can be used to diagnose a patient for cancer, prognosticate a patient with cancer, or to detect the presence or monitor progress of a premalignant condition. The severity of an imbalance as well as the number of regions exhibiting an imbalance can be used. A systematic analysis of non-overlapping segments of a genome can provide a general screening tool for a sample. Additionally, a patient can be tested over time to track severity of each of one or more chromosomal regions and a number of chromosomal regions to enable screening and prognosticating, as well as monitoring of progress (e.g. after treatment).
Chinese University of Hong Kong | Date: 2017-03-30
Methods, systems, and apparatus determine whether a first chromosomal region exhibits a deletion or an amplification associated with cancer in a sample from a subject (e.g., where the sample includes a mixture of cell-free DNA from tumor cells and non-malignant cells. Nucleic acid molecules of the biological sample are sequenced. Respective amounts of a clinically-relevant chromosomal region and of background chromosomal region(s) are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether first chromosomal region exhibits a deletion or an amplification associated with cancer.
Chinese University of Hong Kong | Date: 2017-02-22
This application describes the discovery that, in a pregnant woman, certain genes (such as RASSFIA, APC, CASP8, RARB, SCGB3A1, DAB2IP, PTPN6, THYl, TMEFF2, and PYCARD) originated from a fetus are highly methylated, whereas the same genes of maternal origin are unmethylated. This discovery allows the easy detection of one or more of these methylated fetal genes in a biological sample from a pregnant woman, serving as a universal indicator of the presence of fetal DNA in the sample. These fetal methylation markers are particularly useful as positive controls for a non-invasive analytical process during which the quality and quantity of fetal DNA are monitored. These newly identified fetal markers can also be measured directly for diagnosis of certain pregnancy-related conditions.
Chinese University of Hong Kong | Date: 2017-05-03
It provides a method for predicting the risk of an adverse pregnancy or neonatal outcome for a pregnant subject by detecting the elevated level of bacteria from one or more selected bacterial taxa (e.g., genera or species). A kit useful for such a method is also provided. In addition, it provides a method for determining the risk of having advanced cervical dilation and/or premature cervical shortening based on differentially abundant bacterial taxa.
Chinese University of Hong Kong | Date: 2017-05-24
The contributions of different tissues to a DNA mixture are determined using methylation levels at particular genomic sites. Tissue-specific methylation levels of M tissue types can be used to deconvolve mixture methylation levels measured in the DNA mixture, to determine fraction contributions of each of the M tissue types. Various types of genomic sites can be chosen to have particular properties across tissue types and across individuals, so as to provide increased accuracy in determining contributions of the various tissue types. The fractional contributions can be used to detect abnormal contributions of a particular tissue, indicating a disease state for the tissue. A differential in fractional contributions for different sizes of DNA fragments can also be used to identify a diseased state of a particular tissue. A sequence imbalance for a particular chromosomal region can be detected in a particular tissue, e.g., identifying a location of a tumor.
Chinese University of Hong Kong | Date: 2016-09-22
Embodiments of the present invention provide methods, systems, and apparatus for deducing the fetal DNA fraction in maternal plasma without using paternal or fetal genotypes. Maternal genotype information may be obtained from a maternal-only DNA sample or may be assumed from shallow-depth sequencing of a biological sample having both maternal and fetal DNA molecules. Because sequencing may be at shallow depths, a locus may have only few reads and may fail to exhibit a non-maternal allele even if a non-maternal allele is present. However, normalized parameters that characterize non-maternal alleles sequenced can be used to provide an accurate estimate of the fetal DNA fraction, even if the amount of non-maternal alleles is in error. Methods described herein may not need high-depth sequencing or enrichment of specific regions. As a result, these methods can be integrated into widely used non-invasive prenatal testing and other diagnostics.
Rosalind Franklin University of Medicine, Science and Chinese University of Hong Kong | Date: 2016-08-11
Disclosed herein are methods and compositions for the delivery of polypeptides, including vaccine candidate polypeptides, into mammalian cells comprising the use of photosensitized trypanosomatid organisms. Also disclosed are methods of treatment of trypanosomatid infections comprising administering phthalocyanine compounds or phthalocyanine-treated trypanosomatid microorganisms as vaccines, as well as and polypeptide delivery vectors comprising phthalocyanine-treated trypanosomatid microorganisms.
Chinese University of Hong Kong | Date: 2017-01-20
A classification of a level of cancer in an organism is determined by analyzing a biological sample of the organism. The biological sample comprises clinically-relevant DNA and other DNA. At least some of the DNA is cell-free in the biological sample. An amount of a first set of DNA fragments from the biological sample corresponding to each of a plurality of sizes is measured. A first value of a first parameter is calculated based on the amounts of DNA fragments at the plurality of sizes. The first value is compared to a reference value. A classification of a level of cancer in the organism is determined based on the comparison.
Chinese University of Hong Kong | Date: 2017-06-14
Whether a fetus has an aneuploidy associated with a first chromosome is detected using ratios of alleles detected in a maternal sample having a mixture of maternal and fetal DNA. DNA from the sample is enriched for target regions associated with polymorphic loci and then sequenced. Polymorphic loci (e.g., single nucleotide polymorphisms) in the target regions with fetal-specific alleles are identified on a first chromosome and on one or more reference chromosomes. A first ratio of the fetal-specific alleles and shared alleles is determined for the loci on the first chromosome. A second ratio of the fetal-specific alleles and shared alleles is determined for the loci on the reference chromosome(s). A third ratio of the first and second ratio can be compared to a cutoff to determine whether an aneuploidy is present, and whether the aneuploidy is maternally-derived or paternally-derived.