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Tamim H Shaikh

TitleProfessor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-PEDS

    Collapse Research 
    Collapse research activities and funding
    R01GM120772     (KWOK, PUI-YAN)Sep 22, 2016 - May 31, 2021
    NIH
    Next Generation Mapping of Complex Genomic Regions involved in Recurrent Structural Variations
    Role: Co-Principal Investigator
    R03DE025363     (SHAIKH, TAMIM H)Jul 1, 2015 - Dec 31, 2017
    NIH
    Genomewide Copy Number Variation Analysis and Association with Facial Shape Variation
    Role: Principal Investigator
    R01GM081519     (SHAIKH, TAMIM H)Jul 1, 2007 - Apr 30, 2013
    NIH
    Copy Number Alterations in Genomic Disorders
    Role: Principal Investigator
    R01GM064725     (SHAIKH, TAMIM H)Jan 1, 2002 - Dec 31, 2007
    NIH
    Evolution of Chromosome-specific Low Copy Repeats
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Yilmaz F, Gurusamy U, Mosley TJ, Hallast P, Kim K, Mostovoy Y, Purcell RH, Shaikh TH, Zwick ME, Kwok PY, Lee C, Mulle JG. High level of complexity and global diversity of the 3q29 locus revealed by optical mapping and long-read sequencing. Genome Med. 2023 05 10; 15(1):35. PMID: 37165454.
      View in: PubMed
    2. Null M, Yilmaz F, Astling D, Yu HC, Cole JB, Hallgr?msson B, Santorico SA, Spritz RA, Shaikh TH, Hendricks AE. Genome-wide analysis of copy number variants and normal facial variation in a large cohort of Bantu Africans. HGG Adv. 2022 Jan 13; 3(1):100082. PMID: 35047866.
      View in: PubMed
    3. Demarest S, Calhoun J, Eschbach K, Yu HC, Mirsky D, Angione K, Shaikh TH, Carvill GL, Benke TA. Whole-exome sequencing and adrenocorticotropic hormone therapy in individuals with infantile spasms. Dev Med Child Neurol. 2022 05; 64(5):633-640. PMID: 35830182.
      View in: PubMed
    4. Vervoort L, Dierckxsens N, Pereboom Z, Capozzi O, Rocchi M, Shaikh TH, Vermeesch JR. 22q11.2 Low Copy Repeats Expanded in the Human Lineage. Front Genet. 2021; 12:706641. PMID: 34335701.
      View in: PubMed
    5. Yilmaz F, Null M, Astling D, Yu HC, Cole J, Santorico SA, Hallgrimsson B, Manyama M, Spritz RA, Hendricks AE, Shaikh TH. Genome-wide copy number variations in a large cohort of bantu African children. BMC Med Genomics. 2021 05 17; 14(1):129. PMID: 34001112.
      View in: PubMed
    6. Mostovoy Y, Yilmaz F, Chow SK, Chu C, Lin C, Geiger EA, Meeks NJL, Chatfield KC, Coughlin CR, Surti U, Kwok PY, Shaikh TH. Genomic regions associated with microdeletion/microduplication syndromes exhibit extreme diversity of structural variation. Genetics. 2021 02 09; 217(2). PMID: 33724415.
      View in: PubMed
    7. Reyes-Nava NG, Yu HC, Coughlin CR, Shaikh TH, Quintana AM. Abnormal expression of GABAA receptor subunits and hypomotility upon loss of gabra1 in zebrafish. Biol Open. 2020 04 13; 9(4). PMID: 32205311.
      View in: PubMed
    8. Demaerel W, Mostovoy Y, Yilmaz F, Vervoort L, Pastor S, Hestand MS, Swillen A, Vergaelen E, Geiger EA, Coughlin CR, Chow SK, McDonald-McGinn D, Morrow B, Kwok PY, Xiao M, Emanuel BS, Shaikh TH, Vermeesch JR. The 22q11 low copy repeats are characterized by unprecedented size and structural variability. Genome Res. 2019 09; 29(9):1389-1401. PMID: 31481461.
      View in: PubMed
    9. Hu T, Kruszka P, Martinez AF, Ming JE, Shabason EK, Raam MS, Shaikh TH, Pineda-Alvarez DE, Muenke M. Cytogenetics and holoprosencephaly: A chromosomal microarray study of 222 individuals with holoprosencephaly. Am J Med Genet C Semin Med Genet. 2018 06; 178(2):175-186. PMID: 30182442.
      View in: PubMed
    10. Shaikh TH. Copy Number Variation Disorders. Curr Genet Med Rep. 2017 Dec; 5(4):183-190. PMID: 29732242.
      View in: PubMed
    11. Quintana AM, Yu HC, Brebner A, Pupavac M, Geiger EA, Watson A, Castro VL, Cheung W, Chen SH, Watkins D, Pastinen T, Skovby F, Appel B, Rosenblatt DS, Shaikh TH. Mutations in THAP11 cause an inborn error of cobalamin metabolism and developmental abnormalities. Hum Mol Genet. 2017 08 01; 26(15):2838-2849. PMID: 28449119.
      View in: PubMed
    12. Scalais E, Osterheld E, Weitzel C, De Meirleir L, Mataigne F, Martens G, Shaikh TH, Coughlin CR, Yu HC, Swanson M, Friederich MW, Scharer G, Helbling D, Wendt-Andrae J, Van Hove JLK. X-Linked Cobalamin Disorder (HCFC1) Mimicking Nonketotic Hyperglycinemia With Increased Both Cerebrospinal Fluid Glycine and Methylmalonic Acid. Pediatr Neurol. 2017 Jun; 71:65-69. PMID: 28363510.
      View in: PubMed
    13. Rachubinski AL, Hepburn S, Elias ER, Gardiner K, Shaikh TH. The co-occurrence of Down syndrome and autism spectrum disorder: is it because of additional genetic variations? Prenat Diagn. 2017 Jan; 37(1):31-36. PMID: 27859447.
      View in: PubMed
    14. Yu HC, Coughlin CR, Geiger EA, Salvador BJ, Elias ER, Cavanaugh JL, Chatfield KC, Miyamoto SD, Shaikh TH. Discovery of a potentially deleterious variant in TMEM87B in a patient with a hemizygous 2q13 microdeletion suggests a recessive condition characterized by congenital heart disease and restrictive cardiomyopathy. Cold Spring Harb Mol Case Stud. 2016 May; 2(3):a000844. PMID: 27148590.
      View in: PubMed
    15. Van Laarhoven PM, Neitzel LR, Quintana AM, Geiger EA, Zackai EH, Clouthier DE, Artinger KB, Ming JE, Shaikh TH. Kabuki syndrome genes KMT2D and KDM6A: functional analyses demonstrate critical roles in craniofacial, heart and brain development. Hum Mol Genet. 2015 Aug 01; 24(15):4443-53. PMID: 25972376.
      View in: PubMed
    16. Mlynarski EE, Sheridan MB, Xie M, Guo T, Racedo SE, McDonald-McGinn DM, Gai X, Chow EW, Vorstman J, Swillen A, Devriendt K, Breckpot J, Digilio MC, Marino B, Dallapiccola B, Philip N, Simon TJ, Roberts AE, Piotrowicz M, Bearden CE, Eliez S, Gothelf D, Coleman K, Kates WR, Devoto M, Zackai E, Heine-Su?er D, Shaikh TH, Bassett AS, Goldmuntz E, Morrow BE, Emanuel BS. Copy-Number Variation of the Glucose Transporter Gene SLC2A3 and Congenital Heart Defects in the 22q11.2 Deletion Syndrome. Am J Hum Genet. 2015 May 07; 96(5):753-64. PMID: 25892112.
      View in: PubMed
    17. Coughlin CR, Scharer GH, Friederich MW, Yu HC, Geiger EA, Creadon-Swindell G, Collins AE, Vanlander AV, Coster RV, Powell CA, Swanson MA, Minczuk M, Van Hove JL, Shaikh TH. Mutations in the mitochondrial cysteinyl-tRNA synthase gene, CARS2, lead to a severe epileptic encephalopathy and complex movement disorder. J Med Genet. 2015 Aug; 52(8):532-40. PMID: 25787132.
      View in: PubMed
    18. Gonzalez-Alegre P, Di Paola J, Wang K, Fabbro S, Yu HC, Shaikh TH, Darbro BW, Bassuk AG. Evaluating Familial Essential Tremor with Novel Genetic Approaches: Is it a Genotyping or Phenotyping Issue? Tremor Other Hyperkinet Mov (N Y). 2014; 4:258. PMID: 25374765.
      View in: PubMed
    19. Quintana AM, Geiger EA, Achilly N, Rosenblatt DS, Maclean KN, Stabler SP, Artinger KB, Appel B, Shaikh TH. Hcfc1b, a zebrafish ortholog of HCFC1, regulates craniofacial development by modulating mmachc expression. Dev Biol. 2014 Dec 01; 396(1):94-106. PMID: 25281006.
      View in: PubMed
    20. Yu HC, Geiger EA, Medne L, Zackai EH, Shaikh TH. An individual with blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) and additional features expands the phenotype associated with mutations in KAT6B. Am J Med Genet A. 2014 Apr; 164A(4):950-7. PMID: 24458743.
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    21. Baker PR, Friederich MW, Swanson MA, Shaikh T, Bhattacharya K, Scharer GH, Aicher J, Creadon-Swindell G, Geiger E, MacLean KN, Lee WT, Deshpande C, Freckmann ML, Shih LY, Wasserstein M, Rasmussen MB, Lund AM, Procopis P, Cameron JM, Robinson BH, Brown GK, Brown RM, Compton AG, Dieckmann CL, Collard R, Coughlin CR, Spector E, Wempe MF, Van Hove JL. Variant non ketotic hyperglycinemia is caused by mutations in LIAS, BOLA3 and the novel gene GLRX5. Brain. 2014 Feb; 137(Pt 2):366-79. PMID: 24334290.
      View in: PubMed
    22. Yu HC, Sloan JL, Scharer G, Brebner A, Quintana AM, Achilly NP, Manoli I, Coughlin CR, Geiger EA, Schneck U, Watkins D, Suormala T, Van Hove JL, Fowler B, Baumgartner MR, Rosenblatt DS, Venditti CP, Shaikh TH. An X-linked cobalamin disorder caused by mutations in transcriptional coregulator HCFC1. Am J Hum Genet. 2013 Sep 05; 93(3):506-14. PMID: 24011988.
      View in: PubMed
    23. Izumi K, Housam R, Kapadia C, Stallings VA, Medne L, Shaikh TH, Kublaoui BM, Zackai EH, Grimberg A. Endocrine phenotype of 6q16.1-q21 deletion involving SIM1 and Prader-Willi syndrome-like features. Am J Med Genet A. 2013 Dec; 161A(12):3137-43. PMID: 24038875.
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    24. Delio M, Pope K, Wang T, Samanich J, Haldeman-Englert CR, Kaplan P, Shaikh TH, Cai J, Marion RW, Morrow BE, Babcock M. Spectrum of elastin sequence variants and cardiovascular phenotypes in 49 patients with Williams-Beuren syndrome. Am J Med Genet A. 2013 Mar; 161A(3):527-33. PMID: 23401415.
      View in: PubMed
    25. Coughlin CR, Scharer GH, Shaikh TH. Clinical impact of copy number variation analysis using high-resolution microarray technologies: advantages, limitations and concerns. Genome Med. 2012; 4(10):80. PMID: 23114084.
      View in: PubMed
    26. Stankiewicz P, Kulkarni S, Dharmadhikari AV, Sampath S, Bhatt SS, Shaikh TH, Xia Z, Pursley AN, Cooper ML, Shinawi M, Paciorkowski AR, Grange DK, Noetzel MJ, Saunders S, Simons P, Summar M, Lee B, Scaglia F, Fellmann F, Martinet D, Beckmann JS, Asamoah A, Platky K, Sparks S, Martin AS, Madan-Khetarpal S, Hoover J, Medne L, Bonnemann CG, Moeschler JB, Vallee SE, Parikh S, Irwin P, Dalzell VP, Smith WE, Banks VC, Flannery DB, Lovell CM, Bellus GA, Golden-Grant K, Gorski JL, Kussmann JL, McGregor TL, Hamid R, Pfotenhauer J, Ballif BC, Shaw CA, Kang SH, Bacino CA, Patel A, Rosenfeld JA, Cheung SW, Shaffer LG. Recurrent deletions and reciprocal duplications of 10q11.21q11.23 including CHAT and SLC18A3 are likely mediated by complex low-copy repeats. Hum Mutat. 2012 Jan; 33(1):165-79. PMID: 21948486.
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    27. Goldmuntz E, Paluru P, Glessner J, Hakonarson H, Biegel JA, White PS, Gai X, Shaikh TH. Microdeletions and microduplications in patients with congenital heart disease and multiple congenital anomalies. Congenit Heart Dis. 2011 Nov-Dec; 6(6):592-602. PMID: 22010865.
      View in: PubMed
    28. Hannibal MC, Buckingham KJ, Ng SB, Ming JE, Beck AE, McMillin MJ, Gildersleeve HI, Bigham AW, Tabor HK, Mefford HC, Cook J, Yoshiura K, Matsumoto T, Matsumoto N, Miyake N, Tonoki H, Naritomi K, Kaname T, Nagai T, Ohashi H, Kurosawa K, Hou JW, Ohta T, Liang D, Sudo A, Morris CA, Banka S, Black GC, Clayton-Smith J, Nickerson DA, Zackai EH, Shaikh TH, Donnai D, Niikawa N, Shendure J, Bamshad MJ. Spectrum of MLL2 (ALR) mutations in 110 cases of Kabuki syndrome. Am J Med Genet A. 2011 Jul; 155A(7):1511-6. PMID: 21671394.
      View in: PubMed
    29. Gai X, Xie HM, Perin JC, Takahashi N, Murphy K, Wenocur AS, D'arcy M, O'Hara RJ, Goldmuntz E, Grice DE, Shaikh TH, Hakonarson H, Buxbaum JD, Elia J, White PS. Rare structural variation of synapse and neurotransmission genes in autism. Mol Psychiatry. 2012 Apr; 17(4):402-11. PMID: 21358714.
      View in: PubMed
    30. Foley AR, Hu Y, Zou Y, Yang M, Medne L, Leach M, Conlin LK, Spinner N, Shaikh TH, Falk M, Neumeyer AM, Bliss L, Tseng BS, Winder TL, B?nnemann CG. Large genomic deletions: a novel cause of Ullrich congenital muscular dystrophy. Ann Neurol. 2011 Jan; 69(1):206-11. PMID: 21280092.
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    31. Dougherty MJ, Wilmoth DM, Tooke LS, Shaikh TH, Gai X, Hakonarson H, Biegel JA. Implementation of high resolution single nucleotide polymorphism array analysis as a clinical test for patients with hematologic malignancies. Cancer Genet. 2011 Jan; 204(1):26-38. PMID: 21356189.
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    32. Shaikh TH, Haldeman-Englert C, Geiger EA, Ponting CP, Webber C. Genes and biological processes commonly disrupted in rare and heterogeneous developmental delay syndromes. Hum Mol Genet. 2011 Mar 01; 20(5):880-93. PMID: 21147756.
      View in: PubMed
    33. Gajecka M, Saitta SC, Gentles AJ, Campbell L, Ciprero K, Geiger E, Catherwood A, Rosenfeld JA, Shaikh T, Shaffer LG. Recurrent interstitial 1p36 deletions: Evidence for germline mosaicism and complex rearrangement breakpoints. Am J Med Genet A. 2010 Dec; 152A(12):3074-83. PMID: 21108392.
      View in: PubMed
    34. Sheridan MB, Kato T, Haldeman-Englert C, Jalali GR, Milunsky JM, Zou Y, Klaes R, Gimelli G, Gimelli S, Gemmill RM, Drabkin HA, Hacker AM, Brown J, Tomkins D, Shaikh TH, Kurahashi H, Zackai EH, Emanuel BS. A palindrome-mediated recurrent translocation with 3:1 meiotic nondisjunction: the t(8;22)(q24.13;q11.21). Am J Hum Genet. 2010 Aug 13; 87(2):209-18. PMID: 20673865.
      View in: PubMed
    35. Girirajan S, Rosenfeld JA, Cooper GM, Antonacci F, Siswara P, Itsara A, Vives L, Walsh T, McCarthy SE, Baker C, Mefford HC, Kidd JM, Browning SR, Browning BL, Dickel DE, Levy DL, Ballif BC, Platky K, Farber DM, Gowans GC, Wetherbee JJ, Asamoah A, Weaver DD, Mark PR, Dickerson J, Garg BP, Ellingwood SA, Smith R, Banks VC, Smith W, McDonald MT, Hoo JJ, French BN, Hudson C, Johnson JP, Ozmore JR, Moeschler JB, Surti U, Escobar LF, El-Khechen D, Gorski JL, Kussmann J, Salbert B, Lacassie Y, Biser A, McDonald-McGinn DM, Zackai EH, Deardorff MA, Shaikh TH, Haan E, Friend KL, Fichera M, Romano C, G?cz J, DeLisi LE, Sebat J, King MC, Shaffer LG, Eichler EE. A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet. 2010 Mar; 42(3):203-9. PMID: 20154674.
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    36. Gai X, Perin JC, Murphy K, O'Hara R, D'arcy M, Wenocur A, Xie HM, Rappaport EF, Shaikh TH, White PS. CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics. BMC Bioinformatics. 2010 Feb 04; 11:74. PMID: 20132550.
      View in: PubMed
    37. Haldeman-Englert CR, Chapman KA, Kruger H, Geiger EA, McDonald-McGinn DM, Rappaport E, Zackai EH, Spinner NB, Shaikh TH. A de novo 8.8-Mb deletion of 21q21.1-q21.3 in an autistic male with a complex rearrangement involving chromosomes 6, 10, and 21. Am J Med Genet A. 2010 Jan; 152A(1):196-202. PMID: 20034085.
      View in: PubMed
    38. McCarthy SE, Makarov V, Kirov G, Addington AM, McClellan J, Yoon S, Perkins DO, Dickel DE, Kusenda M, Krastoshevsky O, Krause V, Kumar RA, Grozeva D, Malhotra D, Walsh T, Zackai EH, Kaplan P, Ganesh J, Krantz ID, Spinner NB, Roccanova P, Bhandari A, Pavon K, Lakshmi B, Leotta A, Kendall J, Lee YH, Vacic V, Gary S, Iakoucheva LM, Crow TJ, Christian SL, Lieberman JA, Stroup TS, Lehtim?ki T, Puura K, Haldeman-Englert C, Pearl J, Goodell M, Willour VL, Derosse P, Steele J, Kassem L, Wolff J, Chitkara N, McMahon FJ, Malhotra AK, Potash JB, Schulze TG, N?then MM, Cichon S, Rietschel M, Leibenluft E, Kustanovich V, Lajonchere CM, Sutcliffe JS, Skuse D, Gill M, Gallagher L, Mendell NR, Craddock N, Owen MJ, O'Donovan MC, Shaikh TH, Susser E, Delisi LE, Sullivan PF, Deutsch CK, Rapoport J, Levy DL, King MC, Sebat J. Microduplications of 16p11.2 are associated with schizophrenia. Nat Genet. 2009 Nov; 41(11):1223-7. PMID: 19855392.
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    39. Haldeman-Englert CR, Naeem T, Geiger EA, Warnock A, Feret H, Ciano M, Davidson SL, Deardorff MA, Zackai EH, Shaikh TH. A 781-kb deletion of 13q12.3 in a patient with Peters plus syndrome. Am J Med Genet A. 2009 Aug; 149A(8):1842-5. PMID: 19610101.
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    40. Shaikh TH, Gai X, Perin JC, Glessner JT, Xie H, Murphy K, O'Hara R, Casalunovo T, Conlin LK, D'Arcy M, Frackelton EC, Geiger EA, Haldeman-Englert C, Imielinski M, Kim CE, Medne L, Annaiah K, Bradfield JP, Dabaghyan E, Eckert A, Onyiah CC, Ostapenko S, Otieno FG, Santa E, Shaner JL, Skraban R, Smith RM, Elia J, Goldmuntz E, Spinner NB, Zackai EH, Chiavacci RM, Grundmeier R, Rappaport EF, Grant SF, White PS, Hakonarson H. High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications. Genome Res. 2009 Sep; 19(9):1682-90. PMID: 19592680.
      View in: PubMed
    41. Elia J, Gai X, Xie HM, Perin JC, Geiger E, Glessner JT, D'arcy M, deBerardinis R, Frackelton E, Kim C, Lantieri F, Muganga BM, Wang L, Takeda T, Rappaport EF, Grant SF, Berrettini W, Devoto M, Shaikh TH, Hakonarson H, White PS. Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes. Mol Psychiatry. 2010 Jun; 15(6):637-46. PMID: 19546859.
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    42. Diskin SJ, Hou C, Glessner JT, Attiyeh EF, Laudenslager M, Bosse K, Cole K, Moss? YP, Wood A, Lynch JE, Pecor K, Diamond M, Winter C, Wang K, Kim C, Geiger EA, McGrady PW, Blakemore AI, London WB, Shaikh TH, Bradfield J, Grant SF, Li H, Devoto M, Rappaport ER, Hakonarson H, Maris JM. Copy number variation at 1q21.1 associated with neuroblastoma. Nature. 2009 Jun 18; 459(7249):987-91. PMID: 19536264.
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    43. Stankiewicz P, Sen P, Bhatt SS, Storer M, Xia Z, Bejjani BA, Ou Z, Wiszniewska J, Driscoll DJ, Maisenbacher MK, Bolivar J, Bauer M, Zackai EH, McDonald-McGinn D, Nowaczyk MM, Murray M, Hustead V, Mascotti K, Schultz R, Hallam L, McRae D, Nicholson AG, Newbury R, Durham-O'Donnell J, Knight G, Kini U, Shaikh TH, Martin V, Tyreman M, Simonic I, Willatt L, Paterson J, Mehta S, Rajan D, Fitzgerald T, Gribble S, Prigmore E, Patel A, Shaffer LG, Carter NP, Cheung SW, Langston C, Shaw-Smith C. Genomic and genic deletions of the FOX gene cluster on 16q24.1 and inactivating mutations of FOXF1 cause alveolar capillary dysplasia and other malformations. Am J Hum Genet. 2009 Jun; 84(6):780-91. PMID: 19500772.
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    44. Jackson EM, Sievert AJ, Gai X, Hakonarson H, Judkins AR, Tooke L, Perin JC, Xie H, Shaikh TH, Biegel JA. Genomic analysis using high-density single nucleotide polymorphism-based oligonucleotide arrays and multiplex ligation-dependent probe amplification provides a comprehensive analysis of INI1/SMARCB1 in malignant rhabdoid tumors. Clin Cancer Res. 2009 Mar 15; 15(6):1923-30. PMID: 19276269.
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    45. Kamath BM, Thiel BD, Gai X, Conlin LK, Munoz PS, Glessner J, Clark D, Warthen DM, Shaikh TH, Mihci E, Piccoli DA, Grant SF, Hakonarson H, Krantz ID, Spinner NB. SNP array mapping of chromosome 20p deletions: genotypes, phenotypes, and copy number variation. Hum Mutat. 2009 Mar; 30(3):371-8. PMID: 19058200.
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    46. Coppinger J, McDonald-McGinn D, Zackai E, Shane K, Atkin JF, Asamoah A, Leland R, Weaver DD, Lansky-Shafer S, Schmidt K, Feldman H, Cohen W, Phalin J, Powell B, Ballif BC, Theisen A, Geiger E, Haldeman-Englert C, Shaikh TH, Saitta S, Bejjani BA, Shaffer LG. Identification of familial and de novo microduplications of 22q11.21-q11.23 distal to the 22q11.21 microdeletion syndrome region. Hum Mol Genet. 2009 Apr 15; 18(8):1377-83. PMID: 19193630.
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    47. Haldeman-Englert CR, Gai X, Perin JC, Ciano M, Halbach SS, Geiger EA, McDonald-McGinn DM, Hakonarson H, Zackai EH, Shaikh TH. A 3.1-Mb microdeletion of 3p21.31 associated with cortical blindness, cleft lip, CNS abnormalities, and developmental delay. Eur J Med Genet. 2009 Jul-Aug; 52(4):265-8. PMID: 19100872.
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    48. Inagaki H, Ohye T, Kogo H, Kato T, Bolor H, Taniguchi M, Shaikh TH, Emanuel BS, Kurahashi H. Chromosomal instability mediated by non-B DNA: cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans. Genome Res. 2009 Feb; 19(2):191-8. PMID: 18997000.
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    49. Keating BJ, Tischfield S, Murray SS, Bhangale T, Price TS, Glessner JT, Galver L, Barrett JC, Grant SF, Farlow DN, Chandrupatla HR, Hansen M, Ajmal S, Papanicolaou GJ, Guo Y, Li M, Derohannessian S, de Bakker PI, Bailey SD, Montpetit A, Edmondson AC, Taylor K, Gai X, Wang SS, Fornage M, Shaikh T, Groop L, Boehnke M, Hall AS, Hattersley AT, Frackelton E, Patterson N, Chiang CW, Kim CE, Fabsitz RR, Ouwehand W, Price AL, Munroe P, Caulfield M, Drake T, Boerwinkle E, Reich D, Whitehead AS, Cappola TP, Samani NJ, Lusis AJ, Schadt E, Wilson JG, Koenig W, McCarthy MI, Kathiresan S, Gabriel SB, Hakonarson H, Anand SS, Reilly M, Engert JC, Nickerson DA, Rader DJ, Hirschhorn JN, Fitzgerald GA. Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS One. 2008; 3(10):e3583. PMID: 18974833.
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    50. Sievert AJ, Jackson EM, Gai X, Hakonarson H, Judkins AR, Resnick AC, Sutton LN, Storm PB, Shaikh TH, Biegel JA. Duplication of 7q34 in pediatric low-grade astrocytomas detected by high-density single-nucleotide polymorphism-based genotype arrays results in a novel BRAF fusion gene. Brain Pathol. 2009 Jul; 19(3):449-58. PMID: 19016743.
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    51. Jalali GR, Vorstman JA, Errami A, Vijzelaar R, Biegel J, Shaikh T, Emanuel BS. Detailed analysis of 22q11.2 with a high density MLPA probe set. Hum Mutat. 2008 Mar; 29(3):433-40. PMID: 18033723.
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    52. Shaffer LG, Theisen A, Bejjani BA, Ballif BC, Aylsworth AS, Lim C, McDonald M, Ellison JW, Kostiner D, Saitta S, Shaikh T. The discovery of microdeletion syndromes in the post-genomic era: review of the methodology and characterization of a new 1q41q42 microdeletion syndrome. Genet Med. 2007 Sep; 9(9):607-16. PMID: 17873649.
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    53. Shaikh TH. Oligonucleotide arrays for high-resolution analysis of copy number alteration in mental retardation/multiple congenital anomalies. Genet Med. 2007 Sep; 9(9):617-25. PMID: 17873650.
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    54. Ballif BC, Hornor SA, Jenkins E, Madan-Khetarpal S, Surti U, Jackson KE, Asamoah A, Brock PL, Gowans GC, Conway RL, Graham JM, Medne L, Zackai EH, Shaikh TH, Geoghegan J, Selzer RR, Eis PS, Bejjani BA, Shaffer LG. Discovery of a previously unrecognized microdeletion syndrome of 16p11.2-p12.2. Nat Genet. 2007 Sep; 39(9):1071-3. PMID: 17704777.
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    55. Jackson EM, Shaikh TH, Zhang F, Wainwright LM, Storm PB, Hakonarson H, Zackai EH, Biegel JA. Atypical teratoid/rhabdoid tumor in a patient with Beckwith-Wiedemann syndrome. Am J Med Genet A. 2007 Aug 01; 143A(15):1767-70. PMID: 17603804.
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    56. Jackson EM, Shaikh TH, Gururangan S, Jones MC, Malkin D, Nikkel SM, Zuppan CW, Wainwright LM, Zhang F, Biegel JA. High-density single nucleotide polymorphism array analysis in patients with germline deletions of 22q11.2 and malignant rhabdoid tumor. Hum Genet. 2007 Sep; 122(2):117-27. PMID: 17541642.
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    57. Shaikh TH, O'Connor RJ, Pierpont ME, McGrath J, Hacker AM, Nimmakayalu M, Geiger E, Emanuel BS, Saitta SC. Low copy repeats mediate distal chromosome 22q11.2 deletions: sequence analysis predicts breakpoint mechanisms. Genome Res. 2007 Apr; 17(4):482-91. PMID: 17351135.
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    58. Ming JE, Geiger E, James AC, Ciprero KL, Nimmakayalu M, Zhang Y, Huang A, Vaddi M, Rappaport E, Zackai EH, Shaikh TH. Rapid detection of submicroscopic chromosomal rearrangements in children with multiple congenital anomalies using high density oligonucleotide arrays. Hum Mutat. 2006 May; 27(5):467-73. PMID: 16619270.
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    59. Inagaki H, Ohye T, Kogo H, Yamada K, Kowa H, Shaikh TH, Emanuel BS, Kurahashi H. Palindromic AT-rich repeat in the NF1 gene is hypervariable in humans and evolutionarily conserved in primates. Hum Mutat. 2005 Oct; 26(4):332-42. PMID: 16116616.
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    60. Morrissette JJ, Medne L, Bentley T, Owens NL, Geiger E, Pipan M, Zackai EH, Shaikh T, Spinner NB. A patient with mosaic partial trisomy 18 resulting from dicentric chromosome breakage. Am J Med Genet A. 2005 Aug 30; 137(2):208-12. PMID: 16082706.
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    61. Gotter AL, Shaikh TH, Budarf ML, Rhodes CH, Emanuel BS. A palindrome-mediated mechanism distinguishes translocations involving LCR-B of chromosome 22q11.2. Hum Mol Genet. 2004 Jan 01; 13(1):103-15. PMID: 14613967.
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    62. Nimmakayalu MA, Gotter AL, Shaikh TH, Emanuel BS. A novel sequence-based approach to localize translocation breakpoints identifies the molecular basis of a t(4;22). Hum Mol Genet. 2003 Nov 01; 12(21):2817-25. PMID: 12952865.
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    63. Kurahashi H, Shaikh T, Takata M, Toda T, Emanuel BS. The constitutional t(17;22): another translocation mediated by palindromic AT-rich repeats. Am J Hum Genet. 2003 Mar; 72(3):733-8. PMID: 12557125.
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    64. Shaikh TH, Kurahashi H, Emanuel BS. Evolutionarily conserved low copy repeats (LCRs) in 22q11 mediate deletions, duplications, translocations, and genomic instability: an update and literature review. Genet Med. 2001 Jan-Feb; 3(1):6-13. PMID: 11339380.
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    65. Alem?n C, Roy-Engel AM, Shaikh TH, Deininger PL. Cis-acting influences on Alu RNA levels. Nucleic Acids Res. 2000 Dec 01; 28(23):4755-61. PMID: 11095687.
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    66. Kurahashi H, Shaikh TH, Emanuel BS. Alu-mediated PCR artifacts and the constitutional t(11;22) breakpoint. Hum Mol Genet. 2000 Nov 01; 9(18):2727-32. PMID: 11063731.
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    67. Kurahashi H, Shaikh TH, Zackai EH, Celle L, Driscoll DA, Budarf ML, Emanuel BS. Tightly clustered 11q23 and 22q11 breakpoints permit PCR-based detection of the recurrent constitutional t(11;22). Am J Hum Genet. 2000 Sep; 67(3):763-8. PMID: 10903930.
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    68. Kurahashi H, Shaikh TH, Hu P, Roe BA, Emanuel BS, Budarf ML. Regions of genomic instability on 22q11 and 11q23 as the etiology for the recurrent constitutional t(11;22). Hum Mol Genet. 2000 Jul 01; 9(11):1665-70. PMID: 10861293.
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    69. Shaikh TH, Kurahashi H, Saitta SC, O'Hare AM, Hu P, Roe BA, Driscoll DA, McDonald-McGinn DM, Zackai EH, Budarf ML, Emanuel BS. Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: genomic organization and deletion endpoint analysis. Hum Mol Genet. 2000 Mar 01; 9(4):489-501. PMID: 10699172.
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    70. Shaikh TH, Budarf ML, Celle L, Zackai EH, Emanuel BS. Clustered 11q23 and 22q11 breakpoints and 3:1 meiotic malsegregation in multiple unrelated t(11;22) families. Am J Hum Genet. 1999 Dec; 65(6):1595-607. PMID: 10577913.
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    71. Saitta SC, McGrath JM, Mensch H, Shaikh TH, Zackai EH, Emanuel BS. A 22q11.2 deletion that excludes UFD1L and CDC45L in a patient with conotruncal and craniofacial defects. Am J Hum Genet. 1999 Aug; 65(2):562-6. PMID: 10417299.
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    72. Shaikh TH, Gottlieb S, Sellinger B, Chen F, Roe BA, Oakey RJ, Emanuel BS, Budarf ML. Characterization of CDC45L: a gene in the 22q11.2 deletion region expressed during murine and human development. Mamm Genome. 1999 Mar; 10(3):322-6. PMID: 10051334.
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    73. Bouyge-Moreau I, Rondeau G, Avet-Loiseau H, Andr? MT, B?zieau S, Ch?rel M, Sale?n S, Cadoret E, Shaikh T, De Angelis MM, Arcot S, Batzer M, Moisan JP, Devilder MC. Construction of a 780-kb PAC, BAC, and cosmid contig encompassing the minimal critical deletion involved in B cell chronic lymphocytic leukemia at 13q14.3. Genomics. 1997 Dec 01; 46(2):183-90. PMID: 9417905.
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    74. Shaikh TH, Roy AM, Kim J, Batzer MA, Deininger PL. cDNAs derived from primary and small cytoplasmic Alu (scAlu) transcripts. J Mol Biol. 1997 Aug 15; 271(2):222-34. PMID: 9268654.
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    75. Shaikh TH, Deininger PL. The role and amplification of the HS Alu subfamily founder gene. J Mol Evol. 1996 Jan; 42(1):15-21. PMID: 8576958.
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    76. Arcot SS, Shaikh TH, Kim J, Bennett L, Alegria-Hartman M, Nelson DO, Deininger PL, Batzer MA. Sequence diversity and chromosomal distribution of "young" Alu repeats. Gene. 1995 Oct 03; 163(2):273-8. PMID: 7590280.
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    77. Batzer MA, Rubin CM, Hellmann-Blumberg U, Alegria-Hartman M, Leeflang EP, Stern JD, Bazan HA, Shaikh TH, Deininger PL, Schmid CW. Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats. J Mol Biol. 1995 Mar 31; 247(3):418-27. PMID: 7714898.
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    78. Batzer MA, Stoneking M, Alegria-Hartman M, Bazan H, Kass DH, Shaikh TH, Novick GE, Ioannou PA, Scheer WD, Herrera RJ, et al. African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci U S A. 1994 Dec 06; 91(25):12288-92. PMID: 7991620.
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    79. Batzer MA, Kilroy GE, Richard PE, Shaikh TH, Desselle TD, Hoppens CL, Deininger PL. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 1990 Dec 11; 18(23):6793-8. PMID: 2175877.
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