Related papers: Estimating heterozygosity from a low-coverage geno…
In forensic genetics, short tandem repeats (STRs) are used for human identification (HID). Degraded biological trace samples with low amounts of short DNA fragments (low-quality DNA samples) pose a challenge for STR typing. Predefined…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls…
We examine the distribution of heterozygous sites in nine European and nine Yoruban individuals whose genomic sequences were made publicly available by Complete Genomics. We show that it is possible to obtain detailed information about…
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample…
Cross-sectional HIV incidence estimation leverages recency test results to determine the HIV incidence of a population of interest, where recency test uses biomarker profiles to infer whether an HIV-positive individual was "recently"…
The multivariate hypergeometric distribution describes sampling without replacement from a discrete population of elements divided into multiple categories. Addressing a gap in the literature, we tackle the challenge of estimating discrete…
Whole-genome sequencing in an isolated population with few founders directly ascertains variants from the population bottleneck that may be rare elsewhere. In such populations, shared haplotypes allow imputation of variants in unsequenced…
Many forensic genetic trace samples are of too low quality to obtain short tandem repeat (STR) DNA profiles as the nuclear DNA they contain is highly degraded (e.g., telogen hairs). Instead, performing shotgun DNA sequencing of such samples…
Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
Capture-recapture methods aim to estimate the size of a closed population on the basis of multiple incomplete enumerations of individuals. In many applications, the individual probability of being recorded is heterogeneous in the…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often…
Disease heterogeneity has been a critical challenge for precision diagnosis and treatment, especially in neurologic and neuropsychiatric diseases. Many diseases can display multiple distinct brain phenotypes across individuals, potentially…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
Clinical adoption of human genome sequencing requires methods with known accuracy of genotype calls at millions or billions of positions across a genome. Previous work showing discordance amongst sequencing methods and algorithms has made…
Polygnicity refers to the phenomenon that multiple genetic variants have a non-zero effect on a complex trait. It is defined as the proportion of genetic variants that have a nonzero effect on the trait. Evaluation of polygenicity can…
Inference of population structure from genetic data plays an important role in population and medical genetics studies. With the advancement and decreasing cost of sequencing technology, the increasingly available whole genome sequencing…