Publications

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2023
Dawood M, Akay G, Mitani T, Marafi D, Fatih JM, Gezdirici A, Najmabadi H, Kahrizi K, Punetha J, Grochowski CM, Du H, Jolly A, Li H, Coban-Akdemir Z, Sedlazeck FJ, Hunter JV, Jhangiani SN, Muzny DM, Pehlivan D, Posey JE, Carvalho CMB, Gibbs RA, Lupski JR. A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly. Am J Med Genet A. 2023 ;191(3):794-804.
Duan R, Marafi D, Xia Z-J, Ng BG, Maroofian R, Sumya FTaher, Saad AK, Du H, Fatih JM, Hunter JV, Elbendary HM, Baig SM, Abdullah U, Ali Z, Efthymiou S, Murphy D, Mitani T, Withers MA, Jhangiani SN, Coban-Akdemir Z, Calame DG, Pehlivan D, Gibbs RA, Posey JE, Houlden H, Lupashin VV, Zaki MS, Freeze HH, Lupski JR. Biallelic missense variants in COG3 cause a congenital disorder of glycosylation with impairment of retrograde vesicular trafficking. J Inherit Metab Dis. 2023 ;46(6):1195-1205.
Faqeih EA, Alghamdi MAli, Almahroos MA, Alharby E, Almuntashri M, Alshangiti AM, Clément P, Calame DG, Qebibo L, Burglen L, Doco-Fenzy M, Mastrangelo M, Torella A, Manti F, Nigro V, Alban Z, Alharbi GSaleh, Hashmi JAmjad, Alraddadi R, Alamri R, Mitani T, Magalie B, Coban-Akdemir Z, Geckinli BBilge, Pehlivan D, Romito A, Karageorgou V, Martini J, Colin E, Bonneau D, Bertoli-Avella A, Lupski JR, Pastore A, Peake RWA, Dallol A, Alfadhel M, Almontashiri NAM. Biallelic variants in HECT E3 paralogs, HECTD4 and UBE3C, encoding ubiquitin ligases cause neurodevelopmental disorders that overlap with Angelman syndrome. Genet Med. 2023 ;25(2):100323.
Du H, Dardas Z, Jolly A, Grochowski CM, Jhangiani SN, Li H, Muzny DM, Fatih JM, Yesil G, Elcioglu NH, Gezdirici A, Marafi D, Pehlivan D, Calame DG, Carvalho CMB, Posey JE, Gambin T, Coban-Akdemir Z, Lupski JR. HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data. Nucleic Acids Res. 2023 ;.
Calame DG, Guo T, Wang C, Garrett L, Jolly A, Dawood M, Kurolap A, Henig NZunz, Fatih JM, Herman I, Du H, Mitani T, Becker L, Rathkolb B, Gerlini R, Seisenberger C, Marschall S, Hunter JV, Gerard A, Heidlebaugh A, Challman T, Spillmann RC, Jhangiani SN, Coban-Akdemir Z, Lalani S, Liu L, Revah-Politi A, Iglesias A, Guzman E, Baugh E, Boddaert N, Rondeau S, Ormieres C, Barcia G, Tan QKG, Thiffault I, Pastinen T, Sheikh K, Biliciler S, Mei D, Melani F, Shashi V, Yaron Y, Steele M, Wakeling E, Østergaard E, Nazaryan-Petersen L, Millan F, Santiago-Sim T, Thevenon J, Bruel A-L, Thauvin-Robinet C, Popp D, Platzer K, Gawlinski P, Wiszniewski W, Marafi D, Pehlivan D, Posey JE, Gibbs RA, Gailus-Durner V, Guerrini R, Fuchs H, de Angelis MHrabě, Hölter SM, Cheung H-H, Gu S, Lupski JR. Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease. Am J Hum Genet. 2023 ;110(8):1394-1413.
Petit F, Longoni M, Wells J, Maser RS, Bogenschutz EL, Dysart MJ, Contreras HTM, Frénois F, Pober BR, Clark RD, Giampietro PF, Ropers HH, Hu H, Loscertales M, Wagner R, Ai X, Brand H, Jourdain A-S, Delrue M-A, Gilbert-Dussardier B, Devisme L, Keren B, McCulley DJ, Qiao L, Hernan R, Wynn J, Scott TM, Calame DG, Coban-Akdemir Z, Hernandez P, Hernandez-Garcia A, Yonath H, Lupski JR, Shen Y, Chung WK, Scott DA, Bult CJ, Donahoe PK, High FA. PLS3 missense variants affecting the actin-binding domains cause X-linked congenital diaphragmatic hernia and body-wall defects. Am J Hum Genet. 2023 ;110(10):1787-1803.
2022
Calame DG, Herman I, Maroofian R, Marshall AE, Donis KCarvalho, Fatih JM, Mitani T, Du H, Grochowski CM, Sousa SB, Gijavanekar C, Bakhtiari S, Ito YA, Rocca C, Hunter JV, V Sutton R, Emrick LT, Boycott KM, Lossos A, Fellig Y, Prus E, Kalish Y, Meiner V, Suerink M, Ruivenkamp C, Muirhead K, Saadi NW, Zaki MS, Bouman A, Barakat TStefan, Skidmore DL, Osmond M, Silva TOliveira, Murphy D, Karimiani EGhayoor, Jamshidi Y, Jaddoa AGhanim, Tajsharghi H, Jin SChih, Abbaszadegan MReza, Ebrahimzadeh-Vesal R, Hosseini S, Alavi S, Bahreini A, Zarean E, Salehi MMehdi, Al-Sannaa NAbbas, Zifarelli G, Bauer P, Robson SC, Coban-Akdemir Z, Travaglini L, Nicita F, Jhangiani SN, Gibbs RA, Posey JE, Kruer MC, Kernohan KD, Saute JAMorales, Houlden H, Vanderver A, Elsea SH, Pehlivan D, Marafi D, Lupski JR. Biallelic Variants in the Ectonucleotidase ENTPD1 Cause a Complex Neurodevelopmental Disorder with Intellectual Disability, Distinct White Matter Abnormalities, and Spastic Paraplegia. Ann Neurol. 2022 ;92(2):304-321.
Penon-Portmann M, Eldomery MK, Potocki L, Marafi D, Posey JE, Coban-Akdemir Z, Harel T, Grochowski CM, Loucks H, Devine WPatrick, Van Ziffle J, Doherty D, Lupski JR, Shieh JT. De novo heterozygous variants in SLC30A7 are a candidate cause for Joubert syndrome. Am J Med Genet A. 2022 ;188(8):2360-2366.
Duan R, Hijazi H, Gulec EYilmaz, Eker HKoçak, Costa SR, Sahin Y, Ocak Z, Isikay S, Ozalp O, Bozdogan S, Aslan H, Elcioglu N, Bertola DR, Gezdirici A, Du H, Fatih JM, Grochowski CM, Akay G, Jhangiani SN, Karaca E, Gu S, Coban-Akdemir Z, Posey JE, Bayram Y, V Sutton R, Carvalho CMB, Pehlivan D, Gibbs RA, Lupski JR. Developmental genomics of limb malformations: Allelic series in association with gene dosage effects contribute to the clinical variability. HGG Adv. 2022 ;3(4):100132.
Ma C, Chen N, Jolly A, Zhao S, Coban-Akdemir Z, Tian W, Kang J, Ye Y, Wang Y, Koch A, Zhang Y, Qin C, Bonilla X, Borel C, Rall K, Chen Z, Jhangiani S, Niu Y, Li X, Qiu G, Zhang S, Luo G, Wu Z, Bacopoulou F, Deligeoroglou E, Zhang TJianguo, Rosenberg C, Gibbs RA, Dietrich JE, Dimas AS, Liu P, Antonarakis SE, Brucker SY, Posey JE, Lupski JR, Wu N, Zhu L. Functional characteristics of a broad spectrum of TBX6 variants in Mayer-Rokitansky-Küster-Hauser syndrome. Genet Med. 2022 ;24(11):2262-2273.
Du H, Jolly A, Grochowski CM, Yuan B, Dawood M, Jhangiani SN, Li H, Muzny DM, Fatih JM, Coban-Akdemir Z, Carlin MEsther, Scheuerle AE, Witzl K, Posey JE, Pendleton M, Harrington E, Juul S, Hastings PJ, Bi W, Gibbs RA, Sedlazeck FJ, Lupski JR, Carvalho CMB, Liu P. The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation. Genome Med. 2022 ;14(1):122.
Zhang C, Jolly A, Shayota BJ, Mazzeu JF, Du H, Dawood M, Soper PCelestino, de Lima ARamalho, Ferreira BMerfort, Coban-Akdemir Z, White J, Shears D, Thomson FRobert, Douglas SLouise, Wainwright A, Bailey K, Wordsworth P, Oldridge M, Lester T, Calder AD, Dumic K, Banka S, Donnai D, Jhangiani SN, Potocki L, Chung WK, Mora S, Northrup H, Ashfaq M, Rosenfeld JA, Mason K, Pollack LC, McConkie-Rosell A, Kelly W, McDonald M, Hauser NS, Leahy P, Powell CM, Boy R, Honjo RSayuri, Kok F, Martelli LR, Filho VOdone, Muzny DM, Gibbs RA, Posey JE, Liu P, Lupski JR, V Sutton R, Carvalho CMB. Novel pathogenic variants and quantitative phenotypic analyses of Robinow syndrome: WNT signaling perturbation and phenotypic variability. HGG Adv. 2022 ;3(1):100074.
Taşdelen E, Calame DG, Akay G, Mitani T, Fatih JM, Herman I, Du H, Coban-Akdemir Z, Marafi D, Jhangiani SN, Posey JE, Gibbs RA, Altıparmak T, Kutlay NYürür, Lupski JR, Pehlivan D. Novel RETREG1 (FAM134B) founder allele is linked to HSAN2B and renal disease in a Turkish family. Am J Med Genet A. 2022 ;188(7):2153-2161.
Lima AR, Ferreira BM, Zhang C, Jolly A, Du H, White JJ, Dawood M, Lins TC, Chiabai MA, van Beusekom E, Cordoba MS, Rosa ECCCaldas, Kayserili H, Kimonis V, Wu E, Mellado C, Aggarwal V, Richieri-Costa A, Brunoni D, Canó TM, Jorge AAL, Kim CA, Honjo R, Bertola DR, Dandalo-Girardi RM, Bayram Y, Gezdirici A, Yilmaz-Gulec E, Gumus E, Yilmaz GC, Okamoto N, Ohashi H, Coban-Akdemir Z, Mitani T, Jhangiani SN, Muzny DM, Regattieri NAP, Pogue R, Pereira RW, Otto PA, Gibbs RA, Ali BR, van Bokhoven H, Brunner HG, V Sutton R, Lupski JR, Vianna-Morgante AM, Carvalho CMB, Mazzeu JF. Phenotypic and mutational spectrum of ROR2-related Robinow syndrome. Hum Mutat. 2022 ;43(7):900-918.
Herman I, Jolly A, Du H, Dawood M, Abdel-Salam GMH, Marafi D, Mitani T, Calame DG, Coban-Akdemir Z, Fatih JM, Hegazy I, Jhangiani SN, Gibbs RA, Pehlivan D, Posey JE, Lupski JR. Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses. Am J Med Genet A. 2022 ;188(3):735-750.
Marafi D, Kozar N, Duan R, Bradley S, Yokochi K, Mutairi FAl, Saadi NWaill, Whalen S, Brunet T, Kotzaeridou U, Choukair D, Keren B, Nava C, Kato M, Arai H, Froukh T, Faqeih EAli, AlAsmari AM, Saleh MM, Vairo FPinto E, Pichurin PN, Klee EW, Schmitz CT, Grochowski CM, Mitani T, Herman I, Calame DG, Fatih JM, Du H, Coban-Akdemir Z, Pehlivan D, Jhangiani SN, Gibbs RA, Miyatake S, Matsumoto N, Wagstaff LJ, Posey JE, Lupski JR, Meijer D, Wagner M. A reverse genetics and genomics approach to gene paralog function and disease: Myokymia and the juxtaparanode. Am J Hum Genet. 2022 ;109(9):1713-1723.
Hijazi H, Reis LM, Pehlivan D, Bernstein JA, Muriello M, Syverson E, Bonner D, Estiar MA, Gan-Or Z, Rouleau GA, Lyulcheva E, Greenhalgh L, Tessarech M, Colin E, Guichet A, Bonneau D, van Jaarsveld RH, Lachmeijer AMA, Ruaud L, Levy J, Tabet A-C, Ploski R, Rydzanicz M, Kępczyński Ł, Połatyńska K, Li Y, Fatih JM, Marafi D, Rosenfeld JA, Coban-Akdemir Z, Bi W, Gibbs RA, Hobson GM, Hunter JV, Carvalho CMB, Posey JE, Semina EV, Lupski JR. TCEAL1 loss-of-function results in an X-linked dominant neurodevelopmental syndrome and drives the neurological disease trait in Xq22.2 deletions. Am J Hum Genet. 2022 ;109(12):2270-2282.
Rodrigues Eda S, Griffith S, Martin R, Antonescu C, Posey JE, Coban-Akdemir Z, Jhangiani SN, Doheny KF, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Sheffer A, Chong JX, Einhorn Y, Cupak M, Sobreira N. Variant-level matching for diagnosis and discovery: Challenges and opportunities. Hum Mutat. 2022 ;43(6):782-790.
2021
Calame DG, Bakhtiari S, Logan R, Coban-Akdemir Z, Du H, Mitani T, Fatih JM, Hunter JV, Herman I, Pehlivan D, Jhangiani SN, Person R, Schnur RE, Jin SChih, Bilguvar K, Posey JE, Koh S, Firouzabadi SG, Alehabib E, Tafakhori A, Esmkhani S, Gibbs RA, Noureldeen MM, Zaki MS, Marafi D, Darvish H, Kruer MC, Lupski JR. Biallelic loss-of-function variants in the splicing regulator NSRP1 cause a severe neurodevelopmental disorder with spastic cerebral palsy and epilepsy. Genet Med. 2021 ;23(12):2455-2460.
Calame DG, Fatih JM, Herman I, Coban-Akdemir Z, Du H, Mitani T, Jhangiani SN, Marafi D, Gibbs RA, Posey JE, Mehta VP, Mohila CA, Abid F, Lotze TE, Pehlivan D, Adesina AM, Lupski JR. Deep clinicopathological phenotyping identifies a previously unrecognized pathogenic EMD splice variant. Ann Clin Transl Neurol. 2021 ;8(10):2052-2058.
Li H, Dawood M, Khayat MM, Farek JR, Jhangiani SN, Khan ZM, Mitani T, Coban-Akdemir Z, Lupski JR, Venner E, Posey JE, Sabo A, Gibbs RA. Exome variant discrepancies due to reference-genome differences. Am J Hum Genet. 2021 ;108(7):1239-1250.
Contreras JLongeri, Ladino MA, Aránguiz K, Mendez GP, Coban-Akdemir Z, Yuan B, Gibbs RA, Burrage LC, Lupski JR, Chinn IK, Vogel TP, Orange JS, M Poli C. Immune Dysregulation Mimicking Systemic Lupus Erythematosus in a Patient With Lysinuric Protein Intolerance: Case Report and Review of the Literature. Front Pediatr. 2021 ;9:673957.
Saad AK, Marafi D, Mitani T, Du H, Rafat K, Fatih JM, Jhangiani SN, Coban-Akdemir Z, Gibbs RA, Pehlivan D, Hunter JV, Posey JE, Zaki MS, Lupski JR. Neurodevelopmental disorder in an Egyptian family with a biallelic ALKBH8 variant. Am J Med Genet A. 2021 ;185(4):1288-1293.
Wohler E, Martin R, Griffith S, Rodrigues Eda S, Antonescu C, Posey JE, Coban-Akdemir Z, Jhangiani SN, Doheny KF, Lupski JR, Valle D, Hamosh A, Sobreira N. PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. Orphanet J Rare Dis. 2021 ;16(1):365.