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Department of Molecular and Human Genetics

Medical Genetics and Genomics Trainee Publications

Master
Content

2020

A framework for an evidence-based gene list relevant to autism spectrum disorder. Schaaf CP, Betancur C, (...) Chen CA, et al. Nat Rev Genet. 2020 Jun; 21(6): 367-376. PMID: 32317787

Phenotypic expansion of Bosch-Boonstra-Schaaf optic atrophy syndrome and further evidence for genotype-phenotype correlations. Rech ME, McCarthy JM, Chen CA, et al. Am J Med Genet A. 2020 Jun; 182(6): 1426-1437. PMID: 32275123

Combination of whole exome sequencing and animal modeling identifies TMPRSS9 as a candidate gene for autism spectrum disorder. Chen CA, Pal R, Yin J, et al. Hum Mol Genet. 2020 Feb 1; 29(3): 459-470. PMID: 31943016

Truncating variants in UBAP1 associated with childhood-onset nonsyndromic hereditary spastic paraplegia. Gu S, Chen CA, Rosenfeld JA, et al. Hum Mutat. 2020 Mar; 41(3): 632-640. PMID: 31696996

Multiple mitochondrial dysfunctions syndrome 1: An unusual cause of developmental pulmonary hypertension. Birjiniuk A, Glinton KE, Villafranco N, Boyer S, Laufman J, Mizerik E, Scott D, Elsea SH, Galambos C, Varghese NP, Scaglia F. Am J Med Genet A. 2020 Apr; 182(4): 755-761. PMID: 31970900

Successful liver transplantation in mitochondrial neurogastrointestinal encephalomyopathy (MNGIE). Kripps K, Nakayuenyongsuk W, Shayota BJ, Berquist W, Gomez-Ospina N, (...), Larson AA. Mol Genet Metab. 2020 May; 130(1): 58-64. PMID: 32173240

2019

Loss of CLTRN function produces a neuropsychiatric disorder and a biochemical phenotype that mimics Hartnup disease. Pillai NR, Yubero D, Shayota BJ, Oyarzábal A, Ghosh R, Sun Q, Azamian MS, Arjona C, Brandi N, Palau F, Lalani SR, Artuch R, García-Cazorla A, Scott DA. Am J Med Genet A. 2019 Dec; 179(12): 2459-2468. PMID: 31520464.

A comprehensive review of the sinuvertebral nerve with clinical applications. Shayota B, Wong TL, Fru D, David G, Iwanaga J, Loukas M, Tubbs RS. Anat Cell Biol. 2019 Jun; 52(2): 128-133. PMID: 31338228

Characterization of the renal phenotype in RMND1-related mitochondrial disease. Shayota BJ, Le NT, Bekheirnia N, Rosenfeld JA, Goldstein AC, Moritz M, Bartholomew DW, Pastore MT, Xia F, Eng C, Yang Y, Lamb DJ, Scaglia F, Braun MC, Bekheirnia MR. Mol Genet Genomic Med. 2019 Dec; 7(12): e973. PMID: 31568715

Liver transplantation in propionic and methylmalonic acidemia: A single center study with literature review. Pillai NR, Stroup BM, Poliner A, Rossetti L, Rawls B, Shayota BJ, Soler-Alfonso C, Tunuguntala HP, Goss J, Craigen W, Scaglia F, Sutton VR, Himes RW, Burrage LC. Mol Genet Metab. 2019 Dec; 128(4): 431-443. PMID: 31757659

Alpha-synuclein is a DNA binding protein that modulates DNA repair with implications for Lewy body disorders. Schaser AJ, Osterberg VR, Dent SE, Stackhouse TL, Wakeham CM, Boutros SW, Weston LJ, Owen N, Weissman TA, Luna E, Raber J, Luk KC, McCullough AK, Woltjer RL, Unni VK. Sci Rep. 2019 Jul 29; 9(1): 10919. PMID: 31358782.

Untargeted Metabolomics for Autism Spectrum Disorders: Current Status and Future Directions. Glinton KE, Elsea SH. Front Psychiatry. 2019 Sep 10; 10: 647. PMID: 31551836

Reanalysis of Clinical Exome Sequencing Data. Liu P, Meng L, Normand EA, Xia F, Song X, Ghazi A, Rosenfeld J, Magoulas PL, Braxton A, Ward P, Dai H, Yuan B, Bi W, Xiao R, Wang X, Chiang T, Vetrini F, He W, Cheng H, (...), Yang Y. N Engl J Med. 2019 Jun 20; 380(25): 2478-2480. PMID: 31216405

Phenotypic and biochemical analysis of an international cohort of individuals with variants in NAA10 and NAA15. Cheng H, Gottlieb L, Marchi E, Kleyner R, Bhardwaj P, (...), Lyon GJ. Hum Mol Genet. 2019 Sep 1; 28(17): 2900-2919. PMID 32027362

Missense variants in TAF1 and developmental phenotypes: challenges of determining pathogenicity. Cheng H, Capponi S, Wakeling E, Marchi E, Li Q, (...); Deciphering Developmental Disorders Study, Wang K, Timmers HTM, Lyon GJ. Hum Mutat. 2019. PMID: 31646703

De novo missense variant in the GTPase effector domain (GED) of DNM1L leads to static encephalopathy and seizures. Assia Batzir N, Bhagwat PK, Eble TN, Liu P, Eng CM, Elsea SH, Robak LA, Scaglia F, Goldman AM, Dhar SU, Wangler MF. Cold Spring Harb Mol Case Stud. 2019 Jun 3;5(3). pii: a003673. doi: 10.1101/mcs.a003673. Print 2019 Jun. PubMed PMID: 30850373; PubMed Central PMCID: PMC6549558.

Phenotypic association of 15q11.2 CNVs of the region of breakpoints 1-2 (BP1-BP2) in a large cohort of samples referred for genetic diagnosis. Mohan KN, Cao Y, Pham J, Cheung SW, Hoffner L, Ou ZZ, Surti U, Cook EH, Beaudet AL. J Hum Genet. 2019 Mar; 64(3): 253-255. doi: 10.1038/s10038-018-0543-7. Epub 2018 Dec 12.  PMID: 30542208.

Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases. Dharmadhikari AV, Ghosh R, Yuan B, Liu P, Dai H, Al Masri S, Scull J, Posey JE, Jiang AH, He W, Vetrini F, Braxton AA, Ward P, Chiang T, Qu C, Gu S, Shaw CA, Smith JL, Lalani S, Stankiewicz P, Cheung SW, Bacino CA, Patel A, Breman AM, Wang X, Meng L, Xiao R, Xia F, Muzny D, Gibbs RA, Beaudet AL, Eng CM, Lupski JR, Yang Y, Bi W. Genome Med. 2019 May 17; 11(1): 30. doi: 10.1186/s13073-019-0639-5. PubMed PMID: 31101064.

Growth characteristics in individuals with osteogenesis imperfecta in North America: results from a multicenter study. Jain M, Tam A, Shapiro JR, Steiner RD, Smith PA, Bober MB, Hart T, Cuthbertson D, Krischer J, Mullins M, Bellur S, Byers PH, Pepin M, Durigova M, Glorieux FH, Rauch F, Lee B, Sutton VR; Members of the Brittle Bone Disorders Consortium*, Nagamani SCS. Genet Med. 2019 Feb; 21(2): 275-283. doi: 10.1038/s41436-018-0045-1. Epub 2018 Jul 4. PubMed PMID: 29970925; PubMed Central PMCID: PMC6320321.

Novel deletion of 6p21.31p21.1 associated with laryngeal cleft, developmental delay, dysmorphic features and vascular anomaly. Pillai NR, Marafi D, Monteiro SA, Parnes M, Chandy BM, Patel A, Bacino CA, Breman AM, Burrage LC. Novel deletion of 6p21.31p21.1 associated with laryngeal cleft, developmental delay, dysmorphic features and vascular anomaly. Eur J Med Genet. 2019 Jun;62(6):103531. doi: 10.1016/j.ejmg.2018.08.012. Epub 2018 Aug 22. PubMed PMID: 30142436.

Review of the phenotypic spectrum associated with haploinsufficiency of MYRF. Rossetti LZ, Glinton K, Yuan B, Liu P, Pillai N, Mizerik E, Magoulas P, Rosenfeld JA, Karaviti L, Sutton VR, Lalani SR, Scott DA. Am J Med Genet A. 2019 Jul;179(7):1376-1382. doi: 10.1002/ajmg.a.61182. Epub 2019 May 8. PubMed PMID: 31069960; PubMed Central PMCID: PMC6557668.

Case report and novel treatment of an autosomal recessive Leigh syndrome caused by short-chain enoyl-CoA hydratase deficiency.
Shayota BJ, Soler-Alfonso C, Bekheirnia MR, Mizerik E, Boyer SW, Xiao R, Yang Y, Elsea SH, Scaglia F. Am J Med Genet A. 2019 May;179(5):803-807. doi: 10.1002/ajmg.a.61074. Epub 2019 Mar 7. PubMed PMID: 30848071.

Behavior and sleep disturbance in Smith-Magenis syndrome. Shayota BJ, Elsea SH. Curr Opin Psychiatry. 2019 Mar;32(2):73-78. PubMed PMID: 30557269

L-Cysteine supplementation prevents liver transplantation in a patient with TRMU deficiency.
Soler-Alfonso C, Pillai N, Cooney E, Mysore KR, Boyer S, Scaglia F. Mol Genet Metab Rep. 2019 Jan 25;19:100453. doi: 10.1016/j.ymgmr.2019.100453. eCollection 2019 Jun. PubMed PMID: 30740308; PubMed Central PMCID: PMC6355510.

2018

An RNAi screen in human cell lines reveals conserved DNA damage repair pathways that mitigate formaldehyde sensitivity. Juarez E, Chambwe N, Tang W, Mitchell AD, Owen N, Kumari A, Monnat RJ Jr, McCullough AK. DNA Repair (Amst). 2018 Dec; 72: 1-9. PMID: 30389308

Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes. Grochowski CM, Gu S, Yuan B, Tcw J, Brennand KJ, Sebat J, Malhotra D, McCarthy S, Rudolph U, Lindstrand A, Chong Z, Levy DL, Lupski JR, Carvalho CMB. Hum Mutat. 2018 Jul; 39(7): 939-946. doi: 10.1002/humu.23537. Epub 2018 May 11. PubMed PMID: 29696747; PubMed Central PMCID: PMC5995661.

Novel deletion of 6p21.31p21.1 associated with laryngeal cleft, developmental delay, dysmorphic features and vascular anomaly. Pillai NR, Marafi D, Monteiro SA, Parnes M, Chandy BM, Patel A, Bacino CA, Breman AM, Burrage LC. Eur J Med Genet. 2018 Aug 22: 103531. PubMed PMID: 30142436.

Chromosomal microarray analysis on uncultured chorionic villus sampling can be complicated by confined placental mosaicism for aneuploidy and microdeletions. Gu S, Jernegan M, Van den Veyver IB, Peacock S, Smith J, Breman A. Prenat Diagn. 2018 Oct; 38(11): 858-865. PubMed PMID: 30094853.

Disturbed phospholipid metabolism in serine biosynthesis defects revealed by metabolomic profiling. Glinton KE, Benke PJ, Lines MA, Geraghty MT, Chakraborty P, Al-Dirbashi OY, Jiang Y, Kennedy AD, Grotewiel MS, Sutton VR, Elsea SH, El-Hattab AW. Mol. Genet. Metab. 2018 Mar; 123(3): 309-316. doi: 10.1016/j.ymgme.2017.12.009 Epub 2017 Dec 12. PubMed PMID: 29269105.

Untargeted metabolomics identifies unique though benign biochemical changes in patients with pathogenic variants in UROC1.

Glinton KE, Levy HL, Kennedy AD, Pappan KL, Elsea SH. Mol Genet Metab Rep. 2018 Dec 29;18:14-18. doi: 10.1016/j.ymgmr.2018.12.005. eCollection 2019 Mar. PubMed PMID: 30619714; PubMed Central PMCID: PMC6312870.

Megaloblastic Anemia Progressing to Severe Thrombotic Microangiopathy in Patients with Disordered Vitamin B(12) Metabolism: Case Reports and Literature Review.
Mullikin D, Pillai N, Sanchez R, O'Donnell-Luria AH, Kritzer A, Tal L, Almannai M, Berry GT, Gambello MJ, Li H, Graham B, Srivaths L, Sutton VR, Grimes A. J Pediatr. 2018 Nov;202:315-319.e2. doi: 10.1016/j.jpeds.2018.06.054. Epub 2018 Jul 26. Review. PubMed PMID: 30057141.

A randomized trial to study the comparative efficacy of phenylbutyrate and benzoate on nitrogen excretion and ureagenesis in healthy volunteers.
Nagamani SCS, Agarwal U, Tam A, Azamian M, McMeans A, Didelija IC, Mohammad MA, Marini JC. Genet Med. 2018 Jul; 20(7): 708-716. doi: 10.1038/gim.2017.167. Epub 2017 Oct 12. PubMed PMID: 29693650; PubMed Central PMCID: PMC5924481.

Functional variants in TBX2 are associated with a syndromic cardiovascular and skeletal developmental disorder. Liu N, Schoch K, Luo X, Pena LDM, Bhavana VH, Kukolich MK, Stringer S, Powis Z, Radtke K, Mroske C, Deak KL, McDonald MT, McConkie-Rosell A, Markert ML, Kranz PG, Stong N, Need AC, Bick D, Amaral MD, Worthey EA, Levy S; Undiagnosed Diseases Network (UDN), Wangler MF, Bellen HJ, Shashi V, Yamamoto S. Hum Mol Genet. 2018 Jul 15; 27(14): 2454-2465. PubMed PMID: 29726930

Neuroimaging findings of extensive sphenoethmoidal dysplasia in NF1. Clin Imaging.
Tam A, Sliepka JM, Bellur S, Bray CD, Lincoln CM, Nagamani SCS. 2018 Sep - Oct; 51: 160-163. doi: 10.1016/j.clinimag.2018.04.017. Epub 2018 May 16. PubMed PMID: 29787982; PubMed Central PMCID: PMC6138553.

The expanding neurological phenotype of DNM1L-related disorders.
Wangler MF, Assia Batzir N, Robak LA, Koenig MK, Bacino CA, Scaglia F, Bellen HJ. Brain. 2018 Apr 1; 141(4): e28. doi: 10.1093/brain/awy024 PubMed PMID: 29529134.

Updated recommendation for the benign stand-alone ACMG/AMP criterion. Ghosh R, Harrison S, Rehm H, Plon S and Biesecker L. Human Mutation 2018, Nov; 39(11): 1525-1530.

2017

Use of Exome Sequencing for Infants in Intensive Care Units: Ascertainment of Severe Single-Gene Disorders and Effect on Medical Management.
Meng L, Pammi M, Saronwala A, Magoulas P, Ghazi AR, Vetrini F, Zhang J, He W, Dharmadhikari AV, Qu C, Ward P, Braxton A, Narayanan S, Ge X, Tokita MJ, Santiago-Sim T, Dai H, Chiang T, Smith H, Azamian MS, Robak L, Bostwick BL, Schaaf CP, Potocki L, Scaglia F, Bacino CA, Hanchard NA, Wangler MF, Scott D, Brown C, Hu J, Belmont JW, Burrage LC, Graham BH, Sutton VR, Craigen WJ, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Muzny DM, Miller MJ, Wang X, Leduc MS, Xiao R, Liu P, Shaw C, Walkiewicz M, Bi W, Xia F, Lee B, Eng CM, Yang Y, Lalani SR. JAMA Pediatr. 2017 Dec 4; 171(12): e173438. doi: 10.1001/jamapediatrics.2017.3438 Epub 2017 Dec 4. PubMed PMID: 28973083.

Generalized metabolic bone disease and fracture risk in Rothmund-Thomson syndrome.
Cao F, Lu L, Abrams SA, Hawthorne KM, Tam A, Jin W, Dawson B, Shypailo R, Liu H, Lee B, Nagamani SCS, Wang LL. Hum Mol Genet. 2017 Aug 15; 26(16): 3046-3055. doi: 10.1093/hmg/ddx178 PubMed PMID: 28486640; PubMed Central PMCID: PMC5886079

Plasma Glutamine Is a Minor Precursor for the Synthesis of Citrulline: A Multispecies Study.
Marini JC, Agarwal U, Didelija IC, Azamian M, Stoll B, Nagamani SC. J Nutr. 2017 Apr; 147(4): 549-555. doi: 10.3945/jn.116.243592 Epub 2017 Mar 8. PubMed PMID: 28275102; PubMed Central PMCID: PMC5368584.

A Recurrent De Novo Nonsense Variant in ZSWIM6 Results in Severe Intellectual Disability without Frontonasal or Limb Malformations.
Palmer EE, Kumar R, Gordon CT, Shaw M, Hubert L, Carroll R, Rio M, Murray L, Leffler M, Dudding-Byth T, Oufadem M, Lalani SR, Lewis AM, Xia F, Tam A, Webster R, Brammah S, Filippini F, Pollard J, Spies J, Minoche AE, Cowley MJ, Risen S, Powell-Hamilton NN, Tusi JE, Immken L, Nagakura H, Bole-Feysot C, Nitschké P, Garrigue A, de Saint Basile G, Kivuva E; DDD Study, Scott RH, Rendon A, Munnich A, Newman W, Kerr B, Besmond C, Rosenfeld JA, Amiel J, Field M, Gecz J. Am J Hum Genet. 2017 Dec 7; 101(6): 995-1005. doi: 10.1016/j.ajhg.2017.10.009 Epub 2017 Nov 30. PubMed PMID: 29198722; PubMed Central PMCID: PMC5812890.

Novel EED mutation in patient with Weaver syndrome.
Cooney E, Bi W, Schlesinger AE, Vinson S, Potocki L. Am J Med Genet A. 2017 Feb;173(2):541-545. doi: 10.1002/ajmg.a.38055. Epub 2016 Nov 21. PubMed PMID: 27868325.

Analyses of SLC13A5-epilepsy patients reveal perturbations of TCA cycle. Bainbridge MN, Cooney E, Miller M, Kennedy AD, Wulff JE, Donti T, Jhangiani SN, Gibbs RA, Elsea SH, Porter BE, Graham BH. Mol Genet Metab. 2017 Aug;121(4):314-319. doi: 10.1016/j.ymgme.2017.06.009. Epub 2017 Jun 24. PubMed PMID: 28673551.

Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines. Ghosh R, Oak N, Plon SE. Genome Biol. 2017 Nov 28; 18(1): 225. doi: 10.1186/s13059-017-1353-5. PubMed PMID: 29179779; PubMed Central PMCID: PMC5704597. Commentary by L Bean and M Hegde in Genome Med. Highlighted as one Best of 2017 articles in Genome biology. 2017; 9: 111.