News Archive
2023
12.2023: Yingchu Lo has posted a preprint on her work with us during her postdoc, on evaluating the accuracies of polygenic score models for anthropometric and metabolic traits in Native Hawaiians! We generally find that polygenic score models trained using the largest GWAS would not transfer well to prediction in Hawaiians, particularly those enriched with Polynesian ancestries, though performance is variable. Congrats Yingchu!
11.2023: New members joining the lab before we wrap up the Fall semester! Indu Sharma is a postdoc who previously working on characterizing isolated populations in India/Himalayas, Indu is interested in examining the signature of selection and its modern day consequences on complex traits and diseases. Eunice Lee joined as a senior research associate. Trained as an environmental epidemiologist, she will incorporate her background in working with environmental variables with genetics data! Welcome Indu and Eunice!
11.2023: Jordan Cahoon's project for evaluating imputation accuracy for populations across the globe received the best poster award at International Genetic Epidemiology Society annual meeting in Nashville, TN! (though unfortunately she could not make it).
11.2023: Charleston Chiang was awarded the early career investigator award by HGG Advances this year, though the credit should really go to Grace Sheng who relentlessly tracked down a QC anomaly impacting only 0.2% of the data, but in the end taught all of us something new in genomic analysis!
11.2023: Our lab is well-represented at the 2023 American Society of Human Genetics meeting, including three posters and a talk from Jalen Langie on her work in admixture mapping for childhood leukemia! Check out the photos and links to posters and presentation here!
10.2023: Caoqi Fan's second chapter of his dissertation is now on bioRxiv! In a method we called gLike, we can obtain maximum likelihood estimates of demographic history parameters based on the genealogical trees from the genetic data. We showed that this method is much more accurate over previous methods based on summary statistics of the genetic data. Please let us know if you have any questions or comments! A tweetorial is here.
10.2023: A pair of preprints from members in the group are officially published! Tsz Fung Chan's method HAMSTA that estimates genome-wide heritability and evaluates biases in test statistics of admixture mapping studies was published in American Journal of Human Genetics, and Soyoung Jeon's paper in constructing and evaluating genome-wide PRS for childhood leukemia was published in HGG Advances! Congrats to Tsz Fung and Soyoung!
9.2023: Our lab has been awarded a R01 grant from NIH/NHGRI (R01HG012605), where we will develop methods leveraging genome-wide genealogies inferred from the genetic data (aka ancestral recombination graph) to gain knowledge about population history and to improve trait mapping. This is the third major grant obtained by the lab over the last three years, thanks so much for everyone involved every step along the way!
9.2023: New members joining the lab! While dear old friends left the lab over the summer, we also have multiple new members joining the lab. These include Xinran Wang, who is taking a year focusing on research before applying for Ph.D. this fall, joins us as a Program Analyst; He Tian, a second year Epidemiology PhD student joining the lab after completing her screening exam; and Ji Tang, a new postdoc interested in developing machine learning methods to address population genetic questions. Welcome Xinran, He, and Ji!
8.2023: Charleston Chiang gave a talk on the "Imputation around the World" project at the International Society of Evolution, Medicine, and Public Health (ISEMPH) annual meeting in Irvine, CA.
7.2023: Bryan Dinh's first author paper is released on bioRxiv! In this study we investigated the recombination landscapes of Native Hawaiians and Polynesian-ancestry individuals, and evaluated the impact of a population-specific recombination map for downstream genetic analyses. The maps are released on github and a tweetorial can be found here! Congrats Bryan!
7.6.2023: Caoqi Fan successfully defended his PhD dissertation titled "Beyond Genotypes: Genealogy-Based Inference of Population Structure and Demographic History." Congrats Dr. Fan!
6.2023: Soyoung Jeon's second chapter of her dissertation, evaluating the efficacy of genomic polygenic risk scores for childhood acute lymphoblastic leukemia in Latino children, is now on medRxiv! Congrats Soyoung!
6.2023: Charleston Chiang is appointed the Associate Director for Center for Genetic Epidemiology!
5.2023: Jordan Cahoon's first author paper (as a 3rd year undergrad!) on investigating the imputation efficacy of TOPMed reference panel across global populations is now on bioRxiv! We found persistent under-performance in certain areas of the world that is not represented in the reference panel. This is a true team effort with contributions from Camellia Rui, Echo Tang, and Chris Simons (all were undergrads when they started on the project), as well as from Jalen Langie, Ying-Chu Lo, and Minhui Chen. Please check out Jordan's tweetorial and let us know if you have any feedback!
5.2023: Our lab is very well represented at the Southern California Evolutionary Genetics and Genomics (SCalE) meeting this year! Jordan Cahoon started with a talk on Imputation efficacy across global human populations, and later Bryan Dinh introduced his abstract on characterizing the recombination landscape in Native Hawaiian through a LD-based recombination map!
4.2023: Tsz Fung Chan's first author paper also dropped on bioRxiv. Co-advised by Nick Mancuso, in this study Tsz Fung described his method HAMSTA that can robustly estimate heritability attributed to local ancestry and used his framework to detect confounding due to fine-scale structure in ancestral populations and to estimate an appropriate significance threshold for admixture mapping. Congrats Tsz Fung! A tweetorial can be found here
4.2023: A new preprint, led by Vivian Link from Doc Edge's group, was posted! In this study we leveraged Caoqi Fan's eGRM method to compute local eGRM and devised an approach to perform genetic mapping, more "directly" on the genealogical trees. With Bryan Dinh's help we demonstrated that this method could detect the CREBRF locus in Native Hawaiian samples that were previously unattainable without direct genotyping! Congrats everyone! A short tweetorial here
4.2023: Jalen Langie has been awarded a F31 predoctoral fellowship from NIH/NCI (F31CA278359)! This fellowship will focus on exploring the impact of genetic ancestry on acute lymphoblastic leukemia risk in Latino populations. Congrats Jalen!
3.2023: Jordan Cahoon was one of only ~400 students nation-wide to win the Barry Goldwater Scholarship! Congrats Jordan for this amazing accomplishment!
2.2023: Jalen Langie presented her project of admixture mapping in a Latino cohort to identify loci associated with childhood leukemia as a poster in the Quantitative Genetics and Genomics Gordon Research Conference! You can find the PDF of the poster here. Any questions or comments are welcomed!
1.13.2023: The first PhD student from our group, Soyoung Jeon, successfully defended her PhD dissertation titled "Understanding Acute Lymphoblastic Leukemia in different ethnic groups in the United States." Congrats Dr. Jeon!
1.2023: The triple-liftOver manuscript was highlighted in this month's HGG Advances with a short interview. It is amazing this paper materialized from a tenacious deep dive into a QC anomaly, which could easily have been ignored.
2022
12.2022: Tsz Fung Chan, co-advised by Nick Mancuso, passed his qualifying exam with flying color! His dissertation will focus on "Inferring Genetic Architecture of Complex Traits in Admixed Populations." Congrats Tsz Fung!
11.2022: Our manuscript reporting a bioinformatic error when converting the genomic coordinates of variants in regions inverted between genome build is now published in Human Genetics and Genomics Advances! The manuscript is led by Xin Sheng with the Multiethnic Cohort, with additional help from Jordan Cahoon. We also devised a light-weight tool called triple-liftOver to identify these variants and correct for the errors!
10.2022: Our lab is well represented in the 2022 American Society of Human Genetics meeting here at LA! This includes 6 posters, which are all available online for anyone interested (see this tweet, this tweet, and this tweet, for pictures and links to posters), and culminated in a platform talk by Soyoung Jeon on her work identifying a Latino-specific variant associated with childhood leukemia that may exhibit signature of positive selection!
8.2022: Our lab has been awarded a R01 grant from NIH/NHGRI (R01HG011646), where we will leverage the evolutionary history to improve trait mapping studies and risk stratification models for Native Hawaiians and other Polynesian-anecstry populations! Any motivated and interested postdocs and students please reach out!
6.2022: A number of our lab members are undertaking internships this summer! Jordan Cahoon is a Cloud Infrastructure Software Engineering intern with Oracle. Echo Tang is a Clinical Operations intern with Arthrosi Therapeutics. Soyoung Jeon is a Translational Research intern in the Therapeutics team at 23andMe. Here's hope for a safe and productive summer!
5.2022: Earlier this semester, Camellia Rui successfully completed her M.S. in Biostatistics thesis titled "A Global View of Disparity in Imputation Resources for Conducting Genetic Studies in Diverse Populations." She graduated this Spring term and will be starting in the Biostatistics Ph.D. program at USC this Fall working with Nick Mancuso and Steven Gazal.
4.2022: Caoqi Fan's first author paper, a genealogical estimate of genetic relationships is now published online at American Journal of Human Genetics! The reviewers loved the paper, calling it "a very important contribution highlighting the power of ARG-based inference for detecting population structure." Congrats Caoqi! You can download a copy of the paper for free using this link (until 6/1/2022), and a tl;dr twitter thread here.
3.2022: Dorcus Kholofelo Malomane has joined our group as a postdoctoral fellow. Dorcus obtained her Ph.D. from University of Goettingen, Germany, working on the population and evolutionary genomics of global chicken populations. She will move into human genetics starting with examining the population structure and patterns of genetic variation in Saudi Arabian populations in collaboration with the Mangul Lab. Welcome Dorcus!
2.2022: We have posted a new preprint demonstrating an error that can occur when imputing variants found within regions that are inverted between genome builds. We also provided a simple tool that can identify variants susceptible to this error from plink files.
2021
12.2021: Caoqi Fan successfully defended his qualifying exam proposal and has now officially advanced to candidacy. Congrats Caoqi!
11.2021: Soyoung Jeon's first author paper, a GWAS for childhood acute lymphoblastic leukemia (ALL) across multiple populations, is now published in Leukemia! The paper also received contributions from Minhui Chen and Tsz Fung Chan from our lab. Congrats Soyoung!
10.2021: Caoqi Fan presented his project on the new genealogy-based statistic for genetic relatedness as a lightning talk in the International Genetic Epidemiology Society (IGES) 2021 virtual meeting. You can find his talk here. This same project also received a Reviewer's Choice Award and was as a Poster Talk in American Society of Human Genetics (ASHG) 2021 virtual meeting. Congrats Caoqi!
10.2021: Charleston Chiang was invited to give a talk in the session on Heterogeneity and Cancer Determinants within the Asian and Pacific Islander Diaspora at the 2021 AACR Conference on the Science of Cancer Health Disparities.
9.2021: Jalen Langie has joined our group for her dissertation research in Epidemiology (genetics track). She will bring her experience from immunology to investigate the genetics and evolution of childhood leukemia. Welcome Jalen!
9.2021: Camellia Rui won the 2021 Provost Fellowship to continue conducting her research in the lab. This school year she will also complete her M.S. degreein Biostatistics. She will be applying to PhD programs this Fall for studies in genetics, biostatistics, and computational biology, so be on the look out, folks!
8.2021: Bryan Dinh has been awarded a F31 predoctoral fellowship from NIH/NHGRI (F31HG012159)! This fellowship will focus on generating genomic resources and references for the genetic investigation of an understudied population, Native Hawaiians. Congrats Bryan!
8.2021: Caoqi Fan has published a new preprint introducing a new genealogy-based statistic for genetic relatedness. We showed this genetic relationship matrix to be able to better delineate recent and fine-scale structure, and would be flexible to detect structure varying across time. This novel approach will have significant implications for all statistical applications utilizing the genetic relationship matrix! Link to the github for software release can be found through our Research page. Any question or comment are welcomed!
8.2021: The Chiang Lab has been awarded the R35 MIRA grant from NIH/NIGMS for early stage investigator (R35GM142783)! We will be looking for interested postdocs and students. Please see "Join.Us" tab for details and reach out to Charleston Chiang if you'd like to join us!
7.2021: Christopher Simons, an undergraduate student on a progressive Masters program in Quantitative Biology at USC Dornsife College of Arts and Sciences has joined the lab! Welcome Christopher!
7.2021: Minhui Chen's new paper demonstrating elevated signal of allele frequency differentiation at height-associated loci across continental populations is now published at the European Journal of Human Genetics! This paper added to the evidence of a signature of polygenic adaptation at height-associated loci among human populations. Congrats, Minhui!
6.2021: Camellia Rui has been awarded the Jennifer Battat Scholarship from the Math Department at USC Dornisife College of Letters, Arts, and Sciences! Congrats Camellia!
6.2021: Xinghu Qin's second preprint of a deep-learning method called DeepGenomeScan to detect candidate regions under selection is now available on bioRxiv!
5.2021: A pair of new preprints from our lab!
The first is the lab's first foray into cancer genomics. Led by graduate student Soyoung Jeon, we performed the currently largest multi-ethnic GWAS for childhood acute lymphoblastic leukemia (ALL). We also constructed a polygenic risk score and contrasted its performance as well as the genetic architecture of ALL between Latinos and non-Latino Whites in our sample.
A second preprint is in collaboration with an incoming postdoc (starting this Fall), Xinghu Qin on utilizing non-linear pattern of genetic variation to further improve inference of population structure over a conventional approach such as the PCA. The method is called Kernel Local Fisher Discriminant Analysis of Principal Components (KLFDAPC).
5.2021: Our lab is represented at Biology of Genomes 2021 virtual conference by Tsz Fung Chan, who is presenting his project on a novel framework to disentangle association signals from ancestry vs. confounding by sub-continental stratification in admixed populations (Abstract #103). Application of this methods include estimating heritability explained by local ancestry and estimating empirically the significance threshold for admixture mapping. Poster can also be accessed here.
4.2021: Our lab is represented at PROBGEN 2021 conference (Probabilistic Modeling in Genomics at CSHL) by Caoqi Fan, who is presenting his project on a novel estimator of genetic relationship matrix based on inferred genome-wide genealogical tree sequences (Abstract #80). Poster can also be accessed here.
4.2021: Ying-Chu Lo has joined our group as a postdoctoral fellow. Ying-Chu is funded by the USC-Taiwan postdoctoral fellowship, and will immediately jump into multiple ongoing projects in the lab. Welcome Ying-Chu!
2.2021: The paper on impact of genetic ancestry on risk of complex traits in Native Hawaiian is now published in PLoS Genetics! The paper is co-led by former M.S. student Hanxiao and former postdoc Meng Lin, with contributions also from Tsz Fung Chan and Bryan Dinh. There is a press release from USC and some media coverage. We learned quite a bit (and are continuing to learn) on how to work with an understudied indigenous population in a respectable and sensitive way, including having the Native Hawaiian Community Advisory Board established by University of Hawaii Cancer Center to review our research proposal and to provide feedback on the manuscript. We look forward to continue this research journey and look forward to more engagement with the community once we are out of this covid pandemic. Any trainee from the community who might be interested in working with us either at the pre- or post-doctoral level please reach out!
1.2021: New semester, we welcome new members joining the lab: Echo Tang, an undergraduate student in Quantitative Biology at USC Dornsife College of Arts and Sciences with a minor in Health Policy, and Jordan Cahoon, an undergraduate student in Computer Science at USC Viterbi School of Engineering. Welcome Echo and Jordan!
2020
12.2020: We are looking for a postdoc to join us! This is a 2 year position with possibility to extend for a 3rd year. Remote working is expected at start, and negotiable after "life is back to normal." Interested applicant please see our Join.Us tab for detail. Official ad is here but the easiest way to apply is to email Charleston with application material or questions. (This is different from the postdoc position we are also looking to hire through the T32 fellowship!)
10.2020: Our group is well-represented at ASHG 2020, including two Reviewer's Choice Abstracts! We have posted full size poster and/or lightning talks here, in case you wish to review for details. Specifically, we have:
Soyoung (Abstract #2385) "Multi-ethnic genome-wide association study to identify novel loci associated with childhood acute lymphoblastic leukemia." PDF or MP4
Caoqi (Abstract #2975) "A genealogical estimate of genetic relationship." PPT
Minhui (Abstract #3013) "Polygenic adaptation at height-associated loci among continental populations." PDF
Feel free to reach out to each presenter directly with any questions or comments on the specific project or research in general!
10.2020: We are looking for a postdoc to join us through the T32 postdoctoral training fellowship shared between USC and University of Hawaii. This is a 2 year position with possibility to extend for a 3rd year. Interested applicant please see our posting on jobRxiv and reach out to Charleston for more details!
10.2020: Minhui published a new preprint on frequency differentiation of height-associated SNPs among global continental populations. In this manuscript we showed that by using height-associated SNPs ascertained from biobank GWAS we can be protected from any confounding due to residual stratification in GWAS summary statistics. We found that these height-associated SNPs exhibit significantly higher level of differentiation among African, European, and East Asian populations, consistent with a signature of polygenic adaptation. Any question or comment are welcomed!
9.2020: The consortium paper on trans-ethnic GWAS of blood cell traits in >700,000 individuals is out in Cell!. It was a fun collaboration where we contributed population genetic analyses to demonstrate the power of GWAS in diverse populations.
9.2020: Camellia was awarded the 2020 Provost Fellowship to conduct research in the lab for this school year. Congrats Camellia!
7.2020: Soyoung gave a lightning talk on her multi-ethnic GWAS on acute lymphoblastic leukemia (ALL) in the International Genetic Epidemiology Society (IGES) 2020 annual meeting. Her lightning talk and poster won one of the three Best Poster Awards. Congratulations Soyoung!
7.2020: Minhui's paper on using Biobank Japan GWAS to investigate polygenic adaptation in Sardinia and Europe is officially out in the July issue of American Journal of Human Genetics (free PDF through link available until 8.21.2020)!
6.2020: Sam and Sydney were funded on a Undergraduate Research Associates Program (URAP) over the summer to conduct research in constructing and analyzing polygenic risk scores for ALL!
6.2020: As we began the summer, two more students joined our group: Bryan Dinh, a Ph.D. student from CBB who just finished a rotation in the lab this Spring, and Camellia Rui, an undergraduate student from Mathematics at USC who will also be completing a progressive M.S. thesis in Biostats with us. Welcome Bryan and Camellia!
5.2020: We are looking for a postdoctoral fellow through the Taiwan-USC Postdoctoral Fellowship Program. Please see their website for eligibility and application process. If you are interested, contact Charleston to discuss about submitting an application.
5.2020: A preprint co-led by Hanxiao and Meng is posted on bioRxiv. This was the bulk of Hanxiao's M.S. thesis, where we investigated the impact of genetic ancestry on risk of complex traits in Native Hawaiians. It is important to note that while we estimated genetic ancestry, these estimates are not without errors at the individual levels, and are correlated with non-genetic factors such as culture, life-style, etc. So please see these tweets to interpret the results with caution!
5.2020: Caoqi presented a poster at Biology of Genomes (virtual) conference on his project a genealogical estimate of genetic relationships. Despite the challenges of not being able to see each other face to face, there were still good discussion!
4-5.2020: To keep the Center of Genetic Epidemiology cohesive during COVID-19, we are organizing a virtual seminar series via zoom with an amazing line-up of speakers from statistical, medical, and population geneticists. Please contact Charleston if you're interested to listen in.
2.2020: The ancient DNA paper from Sardinia that we are a part of and build on top of our previous 2018 paper in Nature Genetics is now published in Nature Communications!
1.2020: Charleston was invited to give a seminar at Department of Genetics, University of Georgia in Athens, GA. It is a department strong in evolutionary biology and filled with exciting research from its faculty and students!
1.2020: Sydney Rashid, an undergraduate student from Quantitative Biology has joined our group as a research assistant! Welcome Sydney!
2019
10-11.2019: Minhui gave a short talk at Bay Area Population Genetics meeting (BAPG XVIII) on his preprint on polygenic adaptation and height. Meng also presented a poster on her preprint about CREBRF locus in Native Hawaiians at ASHG 2019 in Houston!
10.2019: A pair of preprints from the lab is posted on bioRxiv! These are the first two research papers from the group. One led by Minhui on polygenic adaptation of height associated loci in Europe and Sardinia, the other led by Meng on the CREBRF locus in Native Hawaiians in the Multiethnic Cohort. Feel free to get in contact if you have any comments or questions!
9.2019: As we start the new semester, the lab is also growing! This term we welcome three new members joining the lab: Caoqi (Ephraim) Fan (PhD student, CBB), Tsz Fung Chan (PhD student, Epidemiology, co-advised with Nick Mancuso), and Sam Sommerer (Undergraduate student, Quantitative Biology). Welcome Caoqi, Tsz Fung, and Sam!
9.2019: Charleston was invited to give a seminar at International Laboratory for Human Genome Research (LIIGH) in Queretaro, Mexico. It was an enjoyable visit to see an up and coming institute with a core of young and energetic faculty!
8.2019: Our manuscript on leveraging Finnish population history to improve power of rare variant association and to detect novel associations to quantitative cardiometabolic traits is published in Nature! This paper really exemplifies the utility to leverage populations of special population history in human medical genetics, which is the central theme of our research group moving forward!
7.2019: Charleston spoke to reporter from The Scientist about genotyping accuracy of rare variants on genotyping arrays, with implication to DTC genetic testing if these results are returned in raw data format for the consumers to interprety themselves or by third party apps.
7.2019: Charleston is now jointly-appointed to the faculty of Quantitative and Computational Biology Section in the Department of Biological Sciences at USC Dornsife College of Letters, Arts, and Sciences.
6.2019: Meng presented her work on the impact of CREBRF variant in Native Hawaiians and the importance of population-specific imputation panel at the 23andMe Genome Research Day. This is really important prelude to a larger research program in Native Hawaiians!
5.2019: Minhui attended Biology of Genomes conference in Cold Spring Harbor Laboratory and presented a poster on his work on re-examining evidence of polygenic adaptation at height-associated loci. He was constantly bombarded with questions!
4.2019: Through three-hours of gruesome grilling, Soyoung successfully defended her qualifying exam proposal and has now officially advanced to candidacy. Congrats Soyoung!
3.2019: Hanxiao successfully completed her M.S. in Biostatistics thesis titled "The Impact of Global and Local Polynesian Ancestry on Complex Traits in Native Hawaiians" and graduated in the Spring term. She will be starting in a Biostatistics Ph.D. program in UT Health School of Public Health this Fall. Congrats Hanxiao!
2018
11.2018: Our preprint on identifying rare variant associations to 64 cardiometabolic quantitative traits using whole exome sequencing data from 20,000 Finns is now on bioRxiv!
10.2018: Charleston was interviewed by the New York Times for a new genetic study using NIPT data from > 141,000 Chinese women. The new paper confirmed many of the signals we had observed in our MBE paper published earlier this summer, but also included interesting virome work and many more Chinese ethnic minorities.
10.2018: For the second time since 2015, our work on the genetics of Sardinians made the cover of Nature Genetics!
8.2018: Our manuscript on population structure, admixture history, and signals of adaptation of Han Chinese is published online at Mol. Biol. Evol.!
8.2018: As we start the new semester, we are also welcoming new members to the lab! Postdoctoral fellow, Meng (Lemon) Lin, has joined the lab, along with students Hanxiao Sun (M.S. student, Biostatistics) and Soyoung (Elizabeth) Jeon (Ph.D. student, PIBBS, co-advised with Joe Wiemels). Welcome Meng, Hanxiao, and Soyoung!
7.2018: Charleston gave a talk on the population structure and admixture history of Han Chinese in the 2018 Society of Molecular Biology and Evolution (SMBE) meeting at Yokohama, Japan.
5.2018: We are looking for a postdoctoral fellow through the USC-Taiwan Postdoctoral Scholar Program. Interested individuals who are Taiwanese nationals with a recent Ph.D. or others who received Ph.D. in Taiwan are welcomed to apply. Fellow is encouraged to develop projects in our ongoing collaboration with the Taiwanese Biobank. See "Join.Us" tab for more details.
5.2018: Postdoctoral fellow, Minhui Chen, has joined the lab! Welcome Minhui!
4.2018: Charleston organized a symposium on Human Adaptation and Evolution at 1st AsiaEvo meeting in Shen Zhen, China. He also visited Taiwan Biobank, gave talk at the Institute of Biomedical Sciences in Academia Sinica, Taiwan, and Chinese Academy of Science and Max Planck Partnered Institute of Computational Biology in Shanghai, China.
2017
12.2017: Hello World! The Chiang Lab has set up shop at the Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California