Malachi Griffith, Ph.D.,  McDonnell Genome Institute

Research Accomplishments & Interests

Dr. Malachi Griffith is an Assistant Director of the McDonnell Genome Institute and an Assistant Professor in the Department of Genetics. Dr. Griffith's research is focused on the development of genomics, bioinformatics and statistical methods as they apply to the study of cancer biology and medicine. A particular focus of his work is in the translation of genomics data from whole genome, exome and transcriptome sequencing into clinically actionable observations and personalized cancer therapies.

Dr. Griffith is also an instructor for the Canadian Bioinformatics Workshops series. He has received scholarships from the Natural Sciences and Engineering Research Council and was a Junior and Senior Scholar of the Michael Smith Foundation for Health Research. He has also received a Research Studentship from the National Cancer Institute of Canada and Terry Fox Foundation and was ranked #2 nationally in the Biomedical Research Category. Dr. Griffith is currently supported by a K99 pathway to independence grant (NIH K99-HG007940).

Other Biographical Information

Before coming to Washington University Dr. Griffith was a bioinformatics post-doctoral fellow at the BC Cancer Agency Genome Sciences center in Vancouver, British Columbia. He received his Ph.D. (Medical Genetics, 2009) from the University of British Columbia and B.S. (Biochemistry and Biology with Honors, 2002) from the University of Winnipeg.

Complete List of Publications (PubMed)

Selected Publications

Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL, Griffith M. GenVisR: Genomic Visualizations in R. Bioinformatics. 2016 Jun 10. pii: btw325. PMID: 27288499

Griffith M*, Griffith OL*, Krysiak K, Skidmore ZL, Christopher MJ, Klco JM, Ramu A, Lamprecht TL, Wagner AH, Campbell KM, Lesurf R, Hundal J, Zhang J, Spies NC, Ainscough BJ, Larson DE, Heath SE, Fronick C, O'Laughlin S, Fulton RS, Magrini V, McGrath S, Smith SM, Miller CA, Maher CA, Payton JE, Walker JR, Eldred JM, Walter MJ, Link DC, Graubert TA, Westervelt P, Kulkarni S, DiPersio JF, Mardis ER, Wilson RK, Ley TJ. Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia. Exp Hematol. 2016 Jul;44(7):603-13. PMID: 27181063

Hundal J, Carreno BM, Petti AA, Linette GP, Griffith OL, Mardis ER, Griffith M. pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Med. 2016 Jan 29;8(1):11. doi: 10.1186/s13073-016-0264-5. PMID: 26825632

Griffith M*, Miller CA*, Griffith OL, Krysiak K, Skidmore ZL, Ramu A, Walker JR, Dang HX, Trani L, Larson DE, Demeter RT, Wendl MC, McMichael JF, Austin RE, Magrini V, McGrath SD, Ly A, Kulkarni S, Cordes MG, Fronick CC, Fulton RS, Maher CA, Ding L, Klco JM, Mardis ER, Ley TJ, Wilson RK. Optimizing cancer genome sequencing and analysis. Cell Syst. 2015 Sep 23;1(3):210-223. PMID: 26645048

Klco JM, Miller CA, Griffith M, Petti A, Spencer DH, Ketkar-Kulkarni S, Wartman LD, Christopher M, Lamprecht TL, Helton NM, Duncavage EJ, Payton JE, Baty J, Heath SE, Griffith OL, Shen D, Hundal J, Chang GS, Fulton R, O'Laughlin M, Fronick C, Magrini V, Demeter RT, Larson DE, Kulkarni S, Ozenberger BA, Welch JS, Walter MJ, Graubert TA, Westervelt P, Radich JP, Link DC, Mardis ER, DiPersio JF, Wilson RK, Ley TJ. Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia. JAMA. 2015 Aug 25;314(8):811-22. PMID: 26305651

Griffith M, Walker JR, Spies NC, Ainscough BJ, Griffith OL. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud. PLoS Comput Biol. 2015 Aug 6;11(8):e1004393. PMID: 26248053

Griffith M*, Griffith OL*, Smith SM*, Ramu A, Callaway MB, Brummett AM, Kiwala MJ, Coffman AC, Regier AA, Oberkfell BJ, Sanderson GE, Mooney TP, Nutter NG, Belter EA, Du F, Long RL, Abbott TE, Ferguson IT, Morton DL, Burnett MM, Weible JV, Peck JB, Dukes A, McMichael JF, Lolofie JT, Derickson BR, Hundal J, Skidmore ZL, Ainscough BJ, Dees ND, Schierding WS, Kandoth C, Kim KH, Lu C, Harris CC, Maher N, Maher CA, Magrini VJ, Abbott BS, Chen K, Clark E, Das I, Fan X, Hawkins AE, Hepler TG, Wylie TN, Leonard SM, Schroeder WE, Shi X, Carmichael LK, Weil MR, Wohlstadter RW, Stiehr G, McLellan MD, Pohl CS, Miller CA, Koboldt DC, Walker JR, Eldred JM, Larson DE, Dooling DJ, Ding L, Mardis ER, Wilson RK. Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol. 2015 Jul 9;11(7):e1004274. PMID: 26158448

Juric D, Castel P, Griffith M, Griffith OL, Won HH, Ellis H, Ebbesen SH, Ainscough BJ, Ramu A, Iyer G, Shah RH, Huynh T, Mino-Kenudson M, Sgroi D, Isakoff S, Thabet A, Elamine L, Solit DB, Lowe SW, Quadt C, Peters M, Derti A, Schegel R, Huang A, Mardis ER, Berger MF, Baselga J, Scaltriti M. Convergent loss of PTEN leads to clinical resistance to a PI(3)K? inhibitor. Nature. 2015 Feb 12;518(7538):240-4. PMID: 25409150

Griffith M*, Griffith OL*, Coffman AC, Weible JV, Koval J, Das I, McMichael JF, Callaway MB, Eldred J, Subramanian J, Govindan R, Kumar R, Bose R, Ding L, Larson D, Dooling D, Smith S, Ley T, Mardis ER, Wilson RK. DGIdb – Mining the druggable genome for personalized medicine. Nature Methods. 2013 Dec;10(12):1209-10. PMID: 24122041

Griffith M, Mwenifumbo JC, Cheung PY, Paul JE, Pugh TJ, Tang MJ, Chittaranjan S, Morin RD, Asano JK, Ally AA, Miao L, Lee A, Chan SY, Taylor G, Severson T, Hou YC, Griffith OL, Cheng GS, Novik K, Moore R, Luk M, Owen D, Brown CJ, Morin GB, Gill S, Tai IT, Marra MA. Novel mRNA isoforms and mutations of uridine monophosphate synthetase and 5-fluorouracil resistance in colorectal cancer. Pharmacogenomics J. 2012 Jan 17. PMID: 22249354

Griffith M, Griffith OL, Mwenifumbo J, Morin RD, Goya R, Tang MJ, Hou YC, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano JK, Chan SY, Li I, McDonald H, Teague K, Zhao Y, Zeng T, Delaney AD, Hirst M, Morin GB, Jones SJM, Tai IT, Marra MA. Alternative expression analysis by RNA sequencing. Nature Methods. 2010 Oct;7(10):843-847. PMID: 20835245.

Griffith M, Tang MJ, Griffith OL, Morin RD, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Hirst M, Jones SJM, Morin GB, Tai IT and Marra MA. ALEXA – A microarray design platform for alternative expression analysis. Nature Methods. 2008 Feb. 5(2):118. PMID: 18235430.

   

Publications

title citation publication date
Genomic characterisation of HER2-positive breast cancer and response to neoadjuvant trastuzumab and chemotherapy - results from the ACOSOG Z1041 (Alliance) trial. Ann Oncol. 2017 Feb 21. doi: 10.1093/annonc/mdx048. 2017-02-21
Cancer Immunogenomics: Computational Neoantigen Identification and Vaccine Design. Cold Spring Harb Symp Quant Biol. 2017 Apr 7. pii: 030726. doi: 10.1101/sqb.2016.81.030726.
Melorheostosis: Exome sequencing of an associated dermatosis implicates postzygotic mosaicism of mutated KRAS. Bone. 2017 Apr 20. pii: S8756-3282(17)30149-7. doi: 10.1016/j.bone.2017.04.010. 2017-04-20
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer Nat Genet. 2017 Jan 31;49(2):170-174. doi: 10.1038/ng.3774. 2017-01-31
NeoPalAna: Neoadjuvant palbociclib, a cyclin-dependent kinase 4/6 inhibitor, and anastrozole for clinical stage 2 or 3 estrogen receptor positive breast cancer Clin Cancer Res. 2017 Mar 7. pii: clincanres.3206.2016. doi: 10.1158/1078-0432.CCR-16-3206. [Epub ahead of print] 2017-03-07
Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473-483. doi: 10.1182/blood-2016-07-729954. Epub 2016 Nov 14. 1970-08-22
Neoantigens in immunotherapy and personalized vaccines: Implications for head and neck squamous cell carcinoma. Oral Oncol. 2016 Oct 14. pii: S1368-8375(16)30175-0. doi: 10.1016/j.oraloncology.2016.09.010. [Epub ahead of print] 2016-10-14
Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas. Cell Rep. 2016 Sep 27;17(1):249-60. doi: 10.1016/j.celrep.2016.08.076. 1970-08-22
DoCM: a database of curated mutations in cancer. Nat Methods. 2016 Sep 29;13(10):806-7. doi: 10.1038/nmeth.4000. 1970-08-22
CIViC: A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer doi: http://dx.doi.org/10.1101/072892
GenVisR: Genomic Visualizations in R. Bioinformatics. 2016 Jun 10. pii: btw325. [Epub ahead of print] 2016-06-10
A common founding clone with TP53 and PTEN mutations gives rise to a concurrent germ cell tumor and acute megakaryoblastic leukemia Cold Spring Harb Mol Case Stud. 2016 Jan;2(1):a000687. doi: 10.1101/mcs.a000687 2015-01-01
Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia Exp Hematol. 2016 Jul;44(7):603-13. doi: 10.1016/j.exphem.2016.04.011. Epub 2016 May 13 2016-07-01
Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers Nat Commun. 2016 Aug 9;7:12498. doi: 10.1038/ncomms12498 2016-08-09
A genomic analysis of Philadelphia chromosome-negative AML arising in patients with CML Blood Cancer J. 2016 Apr 8;6:e413. doi: 10.1038/bcj.2016.18 2016-04-08
A genomic case study of mixed fibrolamellar hepatocellular carcinoma. Ann Oncol. 2016 Mar 30. pii: mdw135. [Epub ahead of print] 2016-03-30
pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Med. 2016 Jan 29;8(1):11. doi: 10.1186/s13073-016-0264-5. 2016-01-29
Optimizing cancer genome sequencing and analysis. Cell Syst. 2015 Sep 23;1(3):210-223. 2015-09-23
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res. 2015 Nov 17. pii: gkv1203. [Epub ahead of print] 2015-11-17
A phase 1 trial of BKM120 (Buparlisib) in combination with fulvestrant in postmenopausal women with estrogen receptor positive metastatic breast cancer. Clin Cancer Res. 2015 Nov 12. pii: clincanres.1745.2015. [Epub ahead of print] 2015-11-12
RNA Sequencing of Tumor-Associated Microglia Reveals Ccl5 as a Stromal Chemokine Critical for Neurofibromatosis-1 Glioma Growth. Neoplasia. 2015 Oct;17(10):776-88. doi: 10.1016/j.neo.2015.10.002. 2015-10-01
DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Res. 2015 Nov 3. pii: gkv1165. [Epub ahead of print] 2015-11-03
Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia. JAMA. 2015 Aug 25;314(8):811-22. doi: 10.1001/jama.2015.9643. 2015-08-25
Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud. PLoS Comput Biol. 2015 Aug 6;11(8):e1004393. doi: 10.1371/journal.pcbi.1004393. eCollection 2015. 2015-08-06
Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol. 2015 Jul 9;11(7):e1004274. doi: 10.1371/journal.pcbi.1004274. eCollection 2015. 2015-07-09
Erratum to: Modeling precision treatment of breast cancer. Genome Biol. 2015 May 12;16(1):95. doi: 10.1186/s13059-015-0658-5. 2015-05-12
Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo. Cancer Cell. 2015 May 11;27(5):631-43. doi: 10.1016/j.ccell.2015.04.008. 2015-05-11
Convergent loss of PTEN leads to clinical resistance to a PI(3)K? inhibitor. Nature. 2014 Nov 17. doi: 10.1038/nature13948. [Epub ahead of print] 2014-11-17
Clonal architectures and driver mutations in metastatic melanomas. PLoS One. 2014 Nov 13;9(11):e111153. doi: 10.1371/journal.pone.0111153. eCollection 2014. 2014-11-13
U2AF1 Mutations alter sequence specificity of pre-mRNA binding and splicing. Leukemia. 2014 Oct 14. doi: 10.1038/leu.2014.303. [Epub ahead of print] 2014-10-14
RNA-sequencing reveals oligodendrocyte and neuronal transcripts in microglia relevant to central nervous system disease. Glia. 2014 Sep 24. doi: 10.1002/glia.22754. [Epub ahead of print] 2014-09-24
SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution. PLoS Comput Biol. 2014 Aug 7;10(8):e1003665. doi: 10.1371/journal.pcbi.1003665. eCollection 2014. 2014-08-07
cDNA Hybrid Capture Improves Transcriptome Analysis on Low-Input and Archived Samples. J Mol Diagn. 2014 May 8. pii: S1525-1578(14)00072-5. doi: 10.1016/j.jmoldx.2014.03.004. [Epub ahead of print] 2014-05-08
Functional heterogeneity of genetically defined subclones in acute myeloid leukemia. Cancer Cell. 2014 Mar 17;25(3):379-92. doi: 10.1016/j.ccr.2014.01.031. Epub 2014 Mar 6. 2014-03-17
Modeling precision treatment of breast cancer Genome Biol. 2013;14(10):R110. 2013-10-31
F11R Is a Novel Monocyte Prognostic Biomarker for Malignant Glioma. PLoS One. 2013 Oct 11;8(10):e77571. doi: 10.1371/journal.pone.0077571. 2013-10-11
DGIdb: mining the druggable genome. Nat Methods. 2013 Oct 13. doi: 10.1038/nmeth.2689. [Epub ahead of print] 2013-10-13
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics. 2006 Sep 29;7:246. 2006-09-29
Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers Cell. 2012 Sep 14;150(6):1121-34. doi: 10.1016/j.cell.2012.08.024. 2012-09-14