Publications

Selected Publications (chronological order)

1. Rivas MA, Koskela J, Huang H, Stevens C, Avila BE, Haritunians T, Neale B, Kurki M, Ganna A, Graham D. Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. bioRxiv. 2016:077180.

2. Pirinen M, Benner C, Marttinen P, Järvelin M-R, Rivas MA, Ripatti S. biMM: Efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements. bioRxiv. 2016:087932.

3. Tukiainen T, Villani A-C, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A. Landscape of X chromosome inactivation across human tissues. bioRxiv. 2016:073957.

4. Rivas MA, Graham D, Sulem P, Stevens C, Desch N, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F. A protein truncating R179X variant in RNF186 confers protection against ulcerative colitis. Nature Communnications. 2016.

Better off without it? Broken gene may help protect against ulcerative colitis

5. Artomov M, Rivas MA, Genovese G, Daly MJ. Mosaic Mutations in Blood DNA Sequence Are Associated with Solid Tumor Cancers. bioRxiv. 2016:065821.

6. Fuchsberger C, Flannick J, Teslovich TM, Mahajan A, Agarwala V, Gaulton KJ, Ma C, Fontanillas P, Moutsianas L, McCarthy DJ. The genetic architecture of type 2 diabetes. Nature. 2016.

7. Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science. 2015;348(6235):666-9.

GTEx findings reveal new insights into how DNA differences influence gene activity, disease susceptibility

8. Pirinen M, Lappalainen T, Zaitlen NA, Dermitzakis ET, Donnelly P, McCarthy MI, Rivas MA. Assessing allele-specific expression across multiple tissues from RNA-seq read data. Bioinformatics. 2015:btv074.

Un paso más allá del análisis del genoma

9. Rivas MA, Moutsianas L. Power of Rare Variant Aggregate Tests. Assessing Rare Variation in Complex Traits: Springer New York; 2015. p. 185-99.

Assessing Rare Variation in Complex Traits

10. Lappalainen T, Sammeth M, Friedländer MR, AC‘t Hoen P, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 2013;501(7468):506-11.

11. Rivas MA, Pirinen M, Neville MJ, Gaulton KJ, Moutsianas L, Lindgren CM, Karpe F, McCarthy MI, Donnelly P. Assessing association between protein truncating variants and quantitative traits. Bioinformatics. 2013;29(19):2419-26.

Protein truncating variants in APOC3 strongly decrease triglyceride levels

12. Clarke GM, Rivas MA, Morris AP. A flexible approach for the analysis of rare variants allowing for a mixture of effects on binary or quantitative traits. PLoS Genet. 2013;9(8):e1003694.

13. Ruark E, Snape K, Humburg P, Loveday C, Bajrami I, Brough R, Rodrigues DN, Renwick A, Seal S, Ramsay E. Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer. Nature. 2013;493(7432):406-10.

Syzygy also detected 75/80 rare variants (MAF<1%) included in the study as positive controls (24/26 base substitutions, 14/14 insertions, 30/32 deletions and 7/8 complex indels). Thus sensitivity was 99.6% for base substitutions and 94.4% for rare indels. 

 

14. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Del Angel G, Rivas MA, Hanna M. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature genetics. 2011;43(5):491-8.

The recipe for finding human genetic variation

15. Neale BM, Rivas MA, Voight BF, Altshuler D, Devlin B, Orho-Melander M, Kathiresan S, Purcell SM, Roeder K, Daly MJ. Testing for an unusual distribution of rare variants. PLoS Genet. 2011;7(3):e1001322.

Bringing rare variants to light with new technique

16. Rivas MA, Beaudoin M, Gardet A, Stevens C, Sharma Y, Zhang CK, Boucher G, Ripke S, Ellinghaus D, Burtt N. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nature genetics. 2011;43(11):1066-73.

Protein truncating genetic variants that protect against Crohn's disease and ulcerative colitis identified in IL23R and CARD9

 

17. Consortium GP. A map of human genome variation from population-scale sequencing. Nature. 2010;467(7319):1061-73.

Additional Publications (alphabetical order)

18. Ameur A, Enroth S, Johansson Å, Zaboli G, Igl W, Johansson AC, Rivas MA, Daly MJ, Schmitz G, Hicks AA. Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids. The American Journal of Human Genetics. 2012;90(5):809-20.

19. Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR. The landscape of genomic imprinting across diverse adult human tissues. Genome research. 2015;25(7):927-36.

20. Beaudoin M, Goyette P, Boucher G, Lo KS, Rivas MA, Stevens C, Alikashani A, Ladouceur M, Ellinghaus D, Törkvist L. Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis. PLoS Genet. 2013;9(9):e1003723.

21. Beaudoin M, Lo KS, N'Diaye A, Rivas MA, Dubé M-P, Laplante N, Phillips MS, Rioux JD, Tardif J-C, Lettre G. Pooled DNA Re-Sequencing of 68 Myocardial Infaction Candidate Genes in French Canadians. Circulation: Cardiovascular Genetics. 2012:CIRCGENETICS. 112.963165.

22. Calvo SE, Tucker EJ, Compton AG, Kirby DM, Crawford G, Burtt NP, Rivas M, Guiducci C, Bruno DL, Goldberger OA. High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nature genetics. 2010;42(10):851-8.

23. Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, Shaw SY, Wolfish CS, Slavik JM, Cotsapas C. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet. 2008;4(11):e1000287.

24. Chuang L-S, Villaverde N, Hui KY, Mortha A, Rahman A, Levine AP, Haritunians T, Ng SME, Zhang W, Hsu N-Y. A frameshift in CSF2RB predominant among Ashkenazi Jews increases risk for Crohn's disease and reduces monocyte signaling via GM-CSF. Gastroenterology. 2016;151(4):710-23. e2.

25. Clapham KR, Chu AY, Wessel J, Natarajan P, Flannick J, Rivas MA, Sartori S, Mehran R, Baber U, Fuster V. A null mutation in ANGPTL8 does not associate with either plasma glucose or type 2 diabetes in humans. BMC endocrine disorders. 2016;16(1):7.

26. Diogo D, Kurreeman F, Stahl EA, Liao KP, Gupta N, Greenberg JD, Rivas MA, Hickey B, Flannick J, Thomson B. Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis. The American Journal of Human Genetics. 2013;92(1):15-27.

27. Do R, Stitziel NO, Won H-H, Jørgensen AB, Duga S, Merlini PA, Kiezun A, Farrall M, Goel A, Zuk O. Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction. Nature. 2015;518(7537):102-6.

28. Ellinghaus D, Zhang H, Zeissig S, Lipinski S, Till A, Jiang T, Stade B, Bromberg Y, Ellinghaus E, Keller A. Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies. Gastroenterology. 2013;145(2):339-47.

29. Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, Rosenstiel P, Strom TM. Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. Scientific Reports. 2016;6.

30. Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, Bustamante CD, Altshuler DL. Demographic history and rare allele sharing among human populations. Proceedings of the National Academy of Sciences. 2011;108(29):11983-8.

31. Consortium G. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science. 2015;348(6235):648-60.

32. Kirby A, Kang HM, Wade CM, Cotsapas C, Kostem E, Han B, Furlotte N, Kang EY, Rivas M, Bogue MA. Fine mapping in 94 inbred mouse strains using a high-density haplotype resource. Genetics. 2010;185(3):1081-95.

33. Kosmicki JA, Churchhouse CL, Rivas MA, Neale BM. Discovery of rare variants for complex phenotypes. Human genetics. 2016:1-10.

34. Lange LA, Hu Y, Zhang H, Xue C, Schmidt EM, Tang Z-Z, Bizon C, Lange EM, Smith JD, Turner EH. Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. The American Journal of Human Genetics. 2014;94(2):233-45.

35. Lek M, Karczewski K, Minikel E, Samocha K, Banks E, Fennell T, O'Donnell-Luria A, Ware J, Hill A, Cummings B. Analysis of protein-coding genetic variation in 60,706 humans. BioRxiv. 2016:030338.

36. Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, Hasz R, Walters G, Garcia F, Young N. The genotype-tissue expression (GTEx) project. Nature genetics. 2013;45(6):580-5.

37. Mahajan A, Sim X, Ng HJ, Manning A, Rivas MA, Highland HM, Locke AE, Grarup N, Im HK, Cingolani P. Identification and functional characterization of G6PC2 coding variants influencing glycemic traits define an effector transcript at the G6PC2-ABCB11 locus. PLoS Genet. 2015;11(1):e1004876.

38. Majithia AR, Flannick J, Shahinian P, Guo M, Bray M-A, Fontanillas P, Gabriel SB, JHS N, Rosen ED, Altshuler D. Rare variants in PPARG with decreased activity in adipocyte differentiation are associated with increased risk of type 2 diabetes. Proceedings of the National Academy of Sciences. 2014;111(36):13127-32.

39. Marouli E, et al. Rare and low-frequency coding variants alter human adult height. Nature. 2017. doi:10.1038/nature21039

40. McCarthy DJ, Humburg P, Kanapin A, Rivas MA, Gaulton K, Cazier J-B, Donnelly P. Choice of transcripts and software has a large effect on variant annotation. Genome Medicine. 2014;6(3):1.

41. Moutsianas L, Agarwala V, Fuchsberger C, Flannick J, Rivas MA, Gaulton KJ, Albers PK, McVean G, Boehnke M, Altshuler D. The power of gene-based rare variant methods to detect disease-associated variation and test hypotheses about complex disease. PLoS Genet. 2015;11(4):e1005165.

42. Richardson TG, Shihab HA, Rivas MA, McCarthy MI, Campbell C, Timpson NJ, Gaunt TR. A Protein Domain and Family Based Approach to Rare Variant Association Analysis. PloS one. 2016;11(4):e0153803.

43. Visschedijk MC, Alberts R, Mucha S, Deelen P, de Jong DJ, Pierik M, Spekhorst LM, Imhann F, van der Meulen-de AE, van der Woude CJ. Pooled Resequencing of 122 Ulcerative Colitis Genes in a Large Dutch Cohort Suggests Population-Specific Associations of Rare Variants in MUC2. PloS one. 2016;11(8):e0159609.

44. Wood AR, Tuke MA, Nalls M, Hernandez D, Gibbs JR, Lin H, Xu CS, Li Q, Shen J, Jun G. Whole genome sequencing to understand the genetic architecture of common gene expression and biomarker phenotypes. Human molecular genetics. 2014:ddu560.

45. Zhang H, Zeissig S, Lipinski S, Till A, Jiang T, Stade B, Bromberg Y, Ellinghaus E, Keller A, Rivas MA. Association Between Variants of PRDM1 and NDP52 and Crohn's Disease, Based on Exome Sequencing and Functional Studies. 2013.