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"Chong, Kevin"
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Uncertainty in estimating the number of contributors from simulated DNA mixture profiles, with and without allele dropout, from Chinese, Malay, Indian, and Caucasian ethnic populations
by
Chong, Kevin Wai Yin
,
Syn, Christopher Kiu-Choong
in
Alleles
,
Asia - epidemiology
,
China - epidemiology
2021
Determining the number of contributors (NOC) accurately in a forensic DNA mixture profile can be challenging. To address this issue, there have been various studies that examined the uncertainty in estimating the NOC in a DNA mixture profile. However, the focus of these studies lies primarily on dominant populations residing within Europe and North America. Thus, there is limited representation of Asian populations in these studies. Further, the effects of allele dropout on the NOC estimation has not been explored. As such, this study assesses the uncertainty of NOC in simulated DNA mixture profiles of Chinese, Malay, and Indian populations, which are the predominant ethnic populations in Asia. The Caucasian ethnic population was also included to provide a basis of comparison with other similar studies. Our results showed that without considering allele dropout, the NOC from DNA mixture profiles derived from up to four contributors of the same ethnic population could be estimated with confidence in the Chinese, Malay, Indian and Caucasian populations. The same results can be observed on DNA mixture profiles originating from a combination of differing ethnic populations. The inclusion of an overall 30% allele dropout rate increased the probability (risk) of underestimating the NOC in a DNA mixture profile; even a 3-person DNA mixture profile has a > 99% risk of underestimating the NOC as two or fewer contributors. However, such risks could be mitigated when the highly polymorphic SE33 locus was included in the dataset. Lastly there was a negligible level of risk in misinterpreting the NOC in a mixture profile as deriving from a single source profile. In summary, our studies showcased novel results representative of the Chinese, Malay, and Indian ethnic populations when examining the uncertainty in NOC estimation in a DNA mixture profile. Our results would be useful in the estimation of NOC in a DNA mixture profile in the Asian context.
Journal Article
The plague
At first it's the dead rats - they start dying in cataclysmic numbers. Then people begin experiencing flu-like symptoms. The masses react in disbelief when the official diagnosis comes in and later, when a quarantine is imposed on the increasingly terrified city. Told with dark humour and an eye trained on the frailties of human behaviour, Chong's novel explores themes in keeping with Albert Camus' original vision - heroism in the face of futility, the psychological strain of quarantine - but fraught with the political and cultural anxieties of our times.
Retraction Note: Uncertainty in estimating the number of contributors from simulated DNA mixture profiles, with and without allele dropout, from Chinese, Malay, Indian, and Caucasian ethnic populations
by
Syn, Christopher Kiu‑Choong
,
Chong, Kevin Wai Yin
in
Humanities and Social Sciences
,
multidisciplinary
,
retraction
2022
Journal Article
The double life of Benson Yu : a novel
\"In a Chinatown housing project lives twelve-year-old Benny, his ailing grandmother, and his strange neighbor Constantine, a man who believes he's a reincarnated medieval samurai. When his grandmother is hospitalized, Benny manages to survive on his own until a social worker comes snooping. With no other family, he is reluctantly taken in by Constantine and soon, an unlikely bond forms between the two. At least, that's what Yu, the narrator of the story, wants to write. The creator of a bestselling comic book, Yu is struggling with continuing the poignant tale of Benny and can't help but interject from the present day, slowly revealing a darker backstory. Can Yu confront the demons he's spent his adult life avoiding or risk his own life...and Benny's?\"--Publisher's description.
The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation
by
Galperin, Michael Y
,
Hauser, Loren
,
Lapidus, Alla
in
Adaptation, Biological
,
Archaea
,
Biomedical and Life Sciences
2009
Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon,
Methanococcoides burtonii
. The genome sequence was manually annotated including the use of a five-tiered evidence rating (ER) system that ranked annotations from ER1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea, which are subject to selection of synonymous codon usage,
M. burtonii
has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino-acid content, while retaining codon usage in common with its mesophilic
Methanosarcina
cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall, membrane, envelope biogenesis COG genes are overrepresented. Likewise, signal transduction (COG category T) genes are overrepresented and
M. burtonii
has a high ‘IQ’ (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two overrepresented COG categories appear to have been acquired from ɛ- and δ-Proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish
M. burtonii
from other archaea, and their genomic characteristics indicate they have an important role in evolving the
M. burtonii
genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have occurred over the last several thousand years as it adapted from a marine to an Antarctic lake environment.
Journal Article
RETRACTED ARTICLE: Uncertainty in estimating the number of contributors from simulated DNA mixture profiles, with and without allele dropout, from Chinese, Malay, Indian, and Caucasian ethnic populations
by
Chong, Kevin Wai Yin
,
Syn, Christopher Kiu-Choong
in
631/114
,
631/208
,
Humanities and Social Sciences
2021
Determining the number of contributors (NOC) accurately in a forensic DNA mixture profile can be challenging. To address this issue, there have been various studies that examined the uncertainty in estimating the NOC in a DNA mixture profile. However, the focus of these studies lies primarily on dominant populations residing within Europe and North America. Thus, there is limited representation of Asian populations in these studies. Further, the effects of allele dropout on the NOC estimation has not been explored. As such, this study assesses the uncertainty of NOC in simulated DNA mixture profiles of Chinese, Malay, and Indian populations, which are the predominant ethnic populations in Asia. The Caucasian ethnic population was also included to provide a basis of comparison with other similar studies. Our results showed that without considering allele dropout, the NOC from DNA mixture profiles derived from up to four contributors of the same ethnic population could be estimated with confidence in the Chinese, Malay, Indian and Caucasian populations. The same results can be observed on DNA mixture profiles originating from a combination of differing ethnic populations. The inclusion of an overall 30% allele dropout rate increased the probability (risk) of underestimating the NOC in a DNA mixture profile; even a 3-person DNA mixture profile has a > 99% risk of underestimating the NOC as two or fewer contributors. However, such risks could be mitigated when the highly polymorphic SE33 locus was included in the dataset. Lastly there was a negligible level of risk in misinterpreting the NOC in a mixture profile as deriving from a single source profile. In summary, our studies showcased novel results representative of the Chinese, Malay, and Indian ethnic populations when examining the uncertainty in NOC estimation in a DNA mixture profile. Our results would be useful in the estimation of NOC in a DNA mixture profile in the Asian context.
Journal Article
A practical study on direct PCR amplification using the GlobalFiler™ PCR Amplification Kit on human bloodstains collected with microFLOQ™ Direct swabs
by
Ng, Boon Kiat
,
Syn, Christopher Kiu Choong
,
Rosli, Afiqah Razanah
in
Amplification
,
blood
,
Bloodstain
2019
•Targeted sample collection using microFLOQ™ Direct swabs requires minimal handling.•Direct PCR amplifications using microFLOQ™ Direct swabs can be used for urgent casework.•DNA results obtained within 3 h from submission for direct amplification.•Direct PCR amplifications is usable for bloodstains on common casework samples.•PCR additives improve peak heights and peak height balance in STR-DNA profile.
Rapid DNA profiling of casework samples is a powerful tool that can support law enforcement agencies in the quick apprehension of perpetrators before they re-offend or escape the jurisdiction. This present study evaluated the feasibility of direct PCR amplification, using the microFLOQ™ Direct swab, for generating DNA profiles (from bloodstains) within 3 h. The swab tip is coated with nylon fibers pre-treated with cell lysing agent, which allows for the direct PCR amplification of collected samples without DNA extraction and quantification, thereby shortening the time required to obtain a DNA profile. Samples collected were directly amplified using GlobalFiler™ PCR Amplification Kit with and without the presence of a PCR additive. Addition of the PCR additive enhanced the peak heights of DNA profiles by approximately 2 fold. Hence, an additive could improve results obtained in the absence of a DNA purification step, especially since casework samples may contain PCR inhibitors. Subsequently, these swabs, amplified using the GlobalFiler™ PCR Amplification Kit with PCR additive, were evaluated on common substrates encountered in routine casework samples submitted with bloodstains, such as denim jeans, knife blade, tissue paper, leather belt, shirt, and blood swabs. The minimum peak heights observed were generally above the analytical and stochastic thresholds established by the laboratory. Finally, the microFLOQ™ Direct swab workflow was compared to the laboratory’s standard workflow of DNA profiling comprising of conventional processing steps such as extraction using the DNA-IQ™ chemistry on Maxwell® 16, followed by quantification, amplification and capillary electrophoresis. The average peak heights of the DNA profiles generated by direct PCR amplification were similar or exceeded those generated using the standard workflow. This study clearly demonstrates that direct PCR amplification using microFLOQ™ Direct swab can be used in a rapid workflow to obtain DNA profiles from casework samples.
Journal Article
Clint Burnham Interviews Kevin Chong
2021
The interview was conducted with Kevin Chong over Zoom for a public audience, primarily students at SFU. Students chose the novel for a pandemic reading group, evidently, for its timeliness but also for its geographic specificity. [...]we have in the audience some students who are in a reading group in November 2020 as well. [...]since I began with a land acknowledgement, I guess that's our first interesting thing to talk about and to ask you about your novel, as your novel begins with a land acknowledgement, not on the copyright page, but actually in the narrative; it's embedded, and it's mentioned a couple of other times as well, when characters give a public speech.
Journal Article
Intraglossal impaction of ingested fish bones: a case series
2010
Although foreign body ingestion and impaction in the pharynx or hypopharynx are quite commonly encountered at our institution, foreign body impaction in tongue tissue is rare. Six cases of foreign bodies embedded in the tongue were identified in a retrospective review spanning the years 1998 to 2007. All the foreign bodies were fish bones. Four of these patients required only tongue exploration to remove the bone; one required a partial glossectomy because of difficulties locating the bone; and one required incision and drainage of an intraglossal abscess that had developed, as well as a tracheostomy. All foreign bodies were successfully removed, with none of the patients experiencing altered sensation or problems with tongue mobility afterwards.
Journal Article