Human Health & Disease

PAST PROJECT

A healthy, optimal life that enables individuals to achieve their personal potential is the goal for us all. Genetics, combined with different environmental interactions, makes every individual unique and the current one-size-fits-all medical solutions, inadequate. Building upon genomic expertise at JCVI, the Center for Human Performance aims to widen our understanding of how individualized markers affect human performance, traits and diseases. Utilizing advanced science and artificial intelligence approaches, we will identify key markers that enable optimal living, as well as risk factors for disease. It is our belief that this research will contribute to advancing the understanding of human health, and will enhance lives beyond managing health risks.

PAST PROJECT

Publications

Proceedings of the National Academy of Sciences of the United States of America. 2020-02-11; 117.6: 3053-3062.

Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging

Hou YC, Yu HC, Martin R, Cirulli ET, Schenker-Ahmed NM, Hicks M, Cohen IV, Jönsson TJ, Heister R, Napier L, Swisher CL, Dominguez S, Tang H, Li W, Perkins BA, Barea J, Rybak C, Smith E, Duchicela K, Doney M, Brar P, Hernandez N, Kirkness EF, Kahn AM, Venter JC, Karow DS, Caskey CT

PMID: 31980526

Genome medicine. 2020-01-10; 12.1: 7.

An unsupervised learning approach to identify novel signatures of health and disease from multimodal data

Shomorony I, Cirulli ET, Huang L, Napier LA, Heister RR, Hicks M, Cohen IV, Yu HC, Swisher CL, Schenker-Ahmed NM, Li W, Nelson KE, Brar P, Kahn AM, Spector TD, Caskey CT, Venter JC, Karow DS, Kirkness EF, Shah N

PMID: 31924279

Proceedings of the National Academy of Sciences of the United States of America. 2019-04-30; 116.18: 8960-8965.

Functional characterization of 3D protein structures informed by human genetic diversity

Hicks M, Bartha I, di Iulio J, Venter JC, Telenti A

PMID: 30988206

Cell metabolism. 2019-02-05; 29.2: 488-500.e2.

Profound Perturbation of the Metabolome in Obesity Is Associated with Health Risk

Cirulli ET, Guo L, Leon Swisher C, Shah N, Huang L, Napier LA, Kirkness EF, Spector TD, Caskey CT, Thorens B, Venter JC, Telenti A

PMID: 30318341

European journal of human genetics : EJHG. 2019-01-01; 27.1: 150-159.

Novel insight into the genetic basis of high-altitude pulmonary hypertension in Kyrgyz highlanders

Iranmehr A, Stobdan T, Zhou D, Poulsen O, Strohl KP, Aldashev A, Telenti A, Wong EHM, Kirkness EF, Venter JC, Bafna V, Haddad GG

PMID: 30254217

Nature genetics. 2018-06-01; 50.6: 790-795.

The fecal metabolome as a functional readout of the gut microbiome

Zierer J, Jackson MA, Kastenmüller G, Mangino M, Long T, Telenti A, Mohney RP, Small KS, Bell JT, Steves CJ, Valdes AM, Spector TD, Menni C

PMID: 29808030

Science (New York, N.Y.). 2018-04-20; 360.6386: 327-331.

Paternally inherited cis-regulatory structural variants are associated with autism

Brandler WM, Antaki D, Gujral M, Kleiber ML, Whitney J, Maile MS, Hong O, Chapman TR, Tan S, Tandon P, Pang T, Tang SC, Vaux KK, Yang Y, Harrington E, Juul S, Turner DJ, Thiruvahindrapuram B, Kaur G, Wang Z, Kingsmore SF, Gleeson JG, Bisson D, Kakaradov B, Telenti A, Venter JC, Corominas R, Toma C, Cormand B, Rueda I, Guijarro S, Messer KS, Nievergelt CM, Arranz MJ, Courchesne E, Pierce K, Muotri AR, Iakoucheva LM, Hervas A, Scherer SW, Corsello C, Sebat J

PMID: 29674594

PLoS genetics. 2018-04-05; 14.4: e1007308.

Comparison of phasing strategies for whole human genomes

Choi Y, Chan AP, Kirkness E, Telenti A, Schork NJ

PMID: 29621242

American journal of human genetics. 2018-04-05; 102.4: 609-619.

Identification of Misclassified ClinVar Variants via Disease Population Prevalence

Shah N, Hou YC, Yu HC, Sainger R, Caskey CT, Venter JC, Telenti A

PMID: 29625023

Proceedings of the National Academy of Sciences of the United States of America. 2018-04-03; 115.14: 3686-3691.

Precision medicine screening using whole-genome sequencing and advanced imaging to identify disease risk in adults

Perkins BA, Caskey CT, Brar P, Dec E, Karow DS, Kahn AM, Hou YC, Shah N, Boeldt D, Coughlin E, Hands G, Lavrenko V, Yu J, Procko A, Appis J, Dale AM, Guo L, Jönsson TJ, Wittmann BM, Bartha I, Ramakrishnan S, Bernal A, Brewer JB, Brewerton S, Biggs WH, Turpaz Y, Venter JC

PMID: 29555771

Scientific reports. 2018-03-12; 8.1: 4333.

Microbial metagenome of urinary tract infection

Moustafa A, Li W, Singh H, Moncera KJ, Torralba MG, Yu Y, Manuel O, Biggs W, Venter JC, Nelson KE, Pieper R, Telenti A

PMID: 29531289

Nature genetics. 2018-03-01; 50.3: 333-337.

The human noncoding genome defined by genetic diversity

di Iulio J, Bartha I, Wong EHM, Yu HC, Lavrenko V, Yang D, Jung I, Hicks MA, Shah N, Kirkness EF, Fabani MM, Biggs WH, Ren B, Venter JC, Telenti A

PMID: 29483654

EBioMedicine. 2018-02-15; 28.316-323.

Acetaminophen (Paracetamol) Use Modifies the Sulfation of Sex Hormones

Cohen IV, Cirulli ET, Mitchell MW, Jonsson TJ, Yu J, Shah N, Spector TD, Guo L, Venter JC, Telenti A

PMID: 29398597

Clinical and translational gastroenterology. 2018-01-18; 9.1: e132.

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease

Moustafa A, Li W, Anderson EL, Wong EHM, Dulai PS, Sandborn WJ, Biggs W, Yooseph S, Jones MB, Venter JC, Nelson KE, Chang JT, Telenti A, Boland BS

PMID: 29345635

Nature reviews. Genetics. 2018-01-01; 19.1: 51-62.

Human gene essentiality

Bartha I, di Iulio J, Venter JC, Telenti A

PMID: 29082913

Proceedings of the National Academy of Sciences of the United States of America. 2017-09-19; 114.38: 10166-10171.

Identification of individuals by trait prediction using whole-genome sequencing data

Lippert C, Sabatini R, Maher MC, Kang EY, Lee S, Arikan O, Harley A, Bernal A, Garst P, Lavrenko V, Yocum K, Wong T, Zhu M, Yang WY, Chang C, Lu T, Lee CWH, Hicks B, Ramakrishnan S, Tang H, Xie C, Piper J, Brewerton S, Turpaz Y, Telenti A, Roby RK, Och FJ, Venter JC

PMID: 28874526

Proceedings of the National Academy of Sciences of the United States of America. 2017-07-25; 114.30: 8059-8064.

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA

Xie C, Yeo ZX, Wong M, Piper J, Long T, Kirkness EF, Biggs WH, Bloom K, Spellman S, Vierra-Green C, Brady C, Scheuermann RH, Telenti A, Howard S, Brewerton S, Turpaz Y, Venter JC

PMID: 28674023

Cell metabolism. 2017-05-02; 25.5: 1054-1062.e5.

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease

Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC, Nelson KE

PMID: 28467925

BMC genomics. 2017-04-13; 18.1: 296.

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies

Greenwald WW, Klitgord N, Seguritan V, Yooseph S, Venter JC, Garner C, Nelson KE, Li W

PMID: 28407798

Nature genetics. 2017-04-01; 49.4: 568-578.

Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites

Long T, Hicks M, Yu HC, Biggs WH, Kirkness EF, Menni C, Zierer J, Small KS, Mangino M, Messier H, Brewerton S, Turpaz Y, Perkins BA, Evans AM, Miller LA, Guo L, Caskey CT, Schork NJ, Garner C, Spector TD, Venter JC, Telenti A

PMID: 28263315

Cancer prevention research (Philadelphia, Pa.). 2017-04-01; 10.4: 226-234.

The Human Microbiome and Cancer

Rajagopala SV, Vashee S, Oldfield LM, Suzuki Y, Venter JC, Telenti A, Nelson KE

PMID: 28096237

PLoS pathogens. 2017-03-22; 13.3: e1006292.

The blood DNA virome in 8,000 humans

Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A

PMID: 28328962

Physiological genomics. 2016-12-01; 48.12: 922-927.

Establishing the involvement of the novel gene AGBL5 in retinitis pigmentosa by whole genome sequencing

Branham K, Matsui H, Biswas P, Guru AA, Hicks M, Suk JJ, Li H, Jakubosky D, Long T, Telenti A, Nariai N, Heckenlively JR, Frazer KA, Sieving PA, Ayyagari R

PMID: 27764769

Proceedings of the National Academy of Sciences of the United States of America. 2016-10-18; 113.42: 11901-11906.

Deep sequencing of 10,000 human genomes

Telenti A, Pierce LC, Biggs WH, di Iulio J, Wong EH, Fabani MM, Kirkness EF, Moustafa A, Shah N, Xie C, Brewerton SC, Bulsara N, Garner C, Metzker G, Sandoval E, Perkins BA, Och FJ, Turpaz Y, Venter JC

PMID: 27702888

Scientific reports. 2016-08-25; 6.31731.

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome

Anderson EL, Li W, Klitgord N, Highlander SK, Dayrit M, Seguritan V, Yooseph S, Biggs W, Venter JC, Nelson KE, Jones MB

PMID: 27558918

Microbiome. 2016-07-30; 4.1: 39.

Microbial diversity in individuals and their household contacts following typical antibiotic courses

Abeles SR, Jones MB, Santiago-Rodriguez TM, Ly M, Klitgord N, Yooseph S, Nelson KE, Pride DT

PMID: 27473422

Cell metabolism. 2016-06-14; 23.6: 949-950.

Dynamics of an Aging Genome

Telenti A, Perkins BA, Venter JC

PMID: 27304490

Proceedings of the National Academy of Sciences of the United States of America. 2015-11-10; 112.45: 14024-9.

Library preparation methodology can influence genomic and functional predictions in human microbiome research

Jones MB, Highlander SK, Anderson EL, Li W, Dayrit M, Klitgord N, Fabani MM, Seguritan V, Green J, Pride DT, Yooseph S, Biggs W, Nelson KE, Venter JC

PMID: 26512100