Soma Das, Ph.D

Professor

Office address: AMB G705A
Telephone number: 773 834 0555

Lab Webpage

Research

The work in our laboratory focuses on the molecular diagnosis of human genetic disease.  Our interest is in translating knowledge obtained from basic research studies to the diagnostic arena, and in developing tools and implementing new technology to improve the diagnosis of human genetic and genomic disease.

My research interests are translational in nature and are an extension of our diagnostic activities.  My main area of interest is in neurodevelopmental disorders, in understanding the underlying molecular basis of these disorders and in genotype-phenotype correlation.  By uncovering the molecular defects in many of these disorders, we have been able to broaden the phenotype associated with many neurodevelopmental genes.  We work on disorders ranging from rare orphan genetic disorders such as Rett and Angelman syndrome to more common disorders such as ataxia.  We use high throughput sequencing techniques, such as exome sequencing, for the identification of disease causing variants. On a more long-term basis we are interested in assessing the diagnostic and clinical utility of high throughput technologies such as whole genome sequencing and transcriptome sequencing in molecular diagnostics.

Selected Publications

Clinical laboratories collaborate to resolve differences in variant interpretations submitted to ClinVar.
Harrison SM, Dolinsky JS, Knight Johnson AE, Pesaran T, Azzariti DR, Bale S, Chao EC, Das S, Vincent L, Rehm HL
(2017 Oct) Genet Med. 2017 Oct;19(10):1096-1104. doi: 10.1038/gim.2017.14. Epub 2017 Mar 16. 28301460 (Full Text)

A novel intronic mutation in MTM1 detected by RNA analysis in a case of X-linked myotubular myopathy.
Al-Hashim A, Gonorazky HD, Amburgey K, Das S, Dowling JJ
(2017 Oct) Neurol Genet. 2017 Aug 24;3(5):e182. doi: 10.1212/NXG.0000000000000182. eCollection 2017 Oct. 28852708 (Full Text)

Reinitiation of mRNA translation in a patient with X-linked infantile spasms with a protein-truncating variant in ARX.
Moey C, Topper S, Karn M, Johnson AK, Das S, Vidaurre J, Shoubridge C
(2016 May) Eur J Hum Genet. 2016 May;24(5):681-9. doi: 10.1038/ejhg.2015.176. Epub 2015 Aug 26. 26306640 (Full Text)

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL
(2015 May) Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5. 25741868 (Full Text)

De novo heterozygous mutations in SMC3 cause a range of Cornelia de Lange syndrome-overlapping phenotypes.
Gil-Rodriguez MC et al.
(2015 Apr) Hum Mutat. 2015 Apr;36(4):454-62. doi: 10.1002/humu.22761. Epub 2015 Mar 17. 25655089

Characterization of patients referred for non-specific intellectual disability testing: the importance of autosomal genes for diagnosis.
Tan CA, Topper S, Del Gaudio D, Nelakuditi V, Shchelochkov O, Nowaczyk MJ, Zeesman S, Brady L, Russell L, Meeks N, Sastry S, Arndt K, Kobiernicki F, Shaw R, Das S
(2015 Feb) Clin Genet. 2015 Feb 19. doi: 10.1111/cge.12575. 25693842

Phenotypic heterogeneity in monogenic diabetes: the clinical and diagnostic utility of a gene panel-based next-generation sequencing approach.
Alkorta-Aranburu G, Carmody D, Cheng YW, Nelakuditi V, Ma L, Dickens JT, Das S, Greeley SAW, Del Gaudio D
(2014 Dec) Mol Genet Metab. 2014 Dec;113(4):315-320. doi: 10.1016/j.ymgme.2014.09.007. Epub 2014 Sep 28. 25306193 (Full Text)

Analysis of ASPM in an ethnically diverse cohort of 400 patient samples: perspectives of the molecular diagnostic laboratory.
Tan CA, del Gaudio D, Dempsey MA, Arndt K, Botes S, Reeder A, Das S
(2014 Apr) Clin Genet. 2014 Apr;85(4):353-8. doi: 10.1111/cge.12172. Epub 2013 May 13. 23611254

Copy number analysis of NIPBL in a cohort of 510 patients reveals rare copy number variants and a mosaic deletion.
Cheng YW, Tan CA, Minor A, Arndt K, Wysinger L, Grange DK, Kozel BA, Robin NH, Waggoner D, Fitzpatrick C, Das S, Del Gaudio D
(2014 Mar) Mol Genet Genomic Med. 2014 Mar;2(2):115-23. doi: 10.1002/mgg3.48. Epub 2013 Nov 14. 24689074 (Full Text)

Two novel RAD21 mutations in patients with mild Cornelia de Lange syndrome-like presentation and report of the first familial case.
Minor A, Shinawi M, Hogue JS, Vineyard M, Hamlin DR, Tan C, Donato K, Wysinger L, Botes S, Das S, Del Gaudio D
(2014 Mar) Gene. 2014 Mar 10;537(2):279-84. doi: 10.1016/j.gene.2013.12.045. Epub 2013 Dec 27. 24378232

Molecular confirmation of nine cases of Cornelia de Lange syndrome diagnosed prenatally.
Dempsey MA, Knight Johnson AE, Swope BS, Moldenhauer JS, Sroka H, Chong K, Chitayat D, Briere L, Lyon H, Palmer N, Gopalani S, Siebert JR, Levesque S, Leblanc J, Menzies D, Haverfield E, Das S
(2014 Feb) Prenat Diagn. 2014 Feb;34(2):163-7. doi: 10.1002/pd.4279. Epub 2013 Dec 9. 24218399

CDKL5 and ARX mutations in males with early-onset epilepsy.
Mirzaa GM, Paciorkowski AR, Marsh ED, Berry-Kravis EM, Medne L, Alkhateeb A, Grix A, Wirrell EC, Powell BR, Nickels KC, Burton B, Paras A, Kim K, Chung W, Dobyns WB, Das S
(2013 May) Pediatr Neurol. 2013 May;48(5):367-77. doi: 10.1016/j.pediatrneurol.2012.12.030. 23583054 (Full Text)

Mutations in STAMBP, encoding a deubiquitinating enzyme, cause microcephaly-capillary malformation syndrome.
McDonell LM, Mirzaa GM, Alcantara D, Schwartzentruber J, Carter MT, Lee LJ, Clericuzio CL, Graham JM Jr, Morris-Rosendahl DJ, Polster T, Acsadi G, Townshend S, Williams S, Halbert A, Isidor B, David A, Smyser CD, Paciorkowski AR, Willing M, Woulfe J, Das S, Beaulieu CL, Marcadier J, Geraghty MT, Frey BJ, Majewski J, Bulman DE, Dobyns WB, O'Driscoll M, Boycott KM
(2013 May) Nat Genet. 2013 May;45(5):556-62. doi: 10.1038/ng.2602. Epub 2013 Mar 31. 23542699 (Full Text)

X-Linked Centronuclear Myopathy
Das, S, Dowling, J, Pierson CR. (October 2011) In: GeneReviews: Genetic Disease Online Reviews at GeneTests-GeneClinics [database online].
Copyright, University of Washington, Seattle. 1997-2011. Available at genetests.org

Exome sequencing and the genetics of intellectual disability.
Topper S, Ober C, Das S
(2011 Aug) Clin Genet. 2011 Aug;80(2):117-26. doi: 10.1111/j.1399-0004.2011.01720.x. Epub 2011 Jun 15. 21627642 (Full Text)

The core FOXG1 syndrome phenotype consists of postnatal microcephaly, severe mental retardation, absent language, dyskinesia, and corpus callosum hypogenesis.
Kortum F, Das S, Flindt M, Morris-Rosendahl DJ, Stefanova I, Goldstein A, Horn D, Klopocki E, Kluger G, Martin P, Rauch A, Roumer A, Saitta S, Walsh LE, Wieczorek D, Uyanik G, Kutsche K, Dobyns WB
(2011 Jun) J Med Genet. 2011 Jun;48(6):396-406. doi: 10.1136/jmg.2010.087528. Epub 2011 Mar 25. 21441262 (Full Text)

LIS1-Associated Lissencephaly/Subcortical Band Heterotopia
Dobyns, WB and Das, SPagon RA, Adam MP, Ardinger HH, et al., editors.
GeneReviews¨ [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2014.
Available from: ncbi.nlm.nih.gov/books/NBK5189

Intragenic deletions and duplications of the LIS1 and DCX genes: a major disease-causing mechanism in lissencephaly and subcortical band heterotopia.
Haverfield EV, Whited AJ, Petras KS, Dobyns WB, Das S
(2009 Jul) Eur J Hum Genet. 2009 Jul;17(7):911-8. doi: 10.1038/ejhg.2008.213. Epub 2008 Dec 3. 19050731 (Full Text)

Molecular genetic testing for ultra rare diseases: models for translation from the research laboratory to the CLIA-certified diagnostic laboratory.
Das S, Bale SJ, Ledbetter DH
(2008 May) Genet Med. 2008 May;10(5):332-6. doi: 10.1097/GIM.0b013e318172838d. 18496031

NSD1 analysis for Sotos syndrome: insights and perspectives from the clinical laboratory.
Waggoner DJ, Raca G, Welch K, Dempsey M, Anderes E, Ostrovnaya I, Alkhateeb A, Kamimura J, Matsumoto N, Schaeffer GB, Martin CL, Das S
(2005 Oct) Genet Med. 2005 Oct;7(8):524-33. doi: 10.1097/01.GIM.0000178503.15559.d3. 16247291