Publications

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2024
Calame DG, Wong JHuixin, Panda P, Nguyen DTuan, Leong NCP, Sangermano R, Patankar SG, Abdel-Hamid M, Alabdi L, Safwat S, Flannery KP, Dardas Z, Fatih JM, Murali C, Kannan V, Lotze TE, Herman I, Ammouri F, Rezich B, Efthymiou S, Alavi S, Murphy D, Firoozfar Z, Nasab MEbrahimi, Bahreini A, Ghasemi M, Haridy NA, Goldouzi HReza, Eghbal F, Karimiani EGhayoor, Srinivasan VM, Gowda VK, Du H, Jhangiani SN, Coban-Akdemir Z, Marafi D, Rodan L, Isikay S, Rosenfeld JA, Ramanathan S, Staton M, Clark RD, Wenman C, Loughlin S, Saad R, Ashraf T, Male A, Tadros S, Boostani R, Abdel-Salam GMH, Zaki M, Abdalla E, M Manzini C, Pehlivan D, Posey JE, Gibbs RA, Houlden H, Alkuraya FS, Bujakowska K, Maroofian R, Lupski JR, Nguyen LNam. Biallelic variation in the choline and ethanolamine transporter underlies a pleiotropic disease spectrum from adult neurodegeneration to severe developmental disorders. medRxiv. 2024 ;.
Mahmoud M, Harting J, Corbitt H, Chen X, Jhangiani SN, Doddapaneni H, Meng Q, Han T, Lambert C, Zhang S, Baybayan P, Henno G, Shen H, Hu J, Han Y, Riegler C, Metcalf GA, Henno G, Chinn IK, Eberle MA, Kingan S, Farinholt T, Carvalho CMB, Gibbs RA, Kronenberg Z, Muzny DM, Sedlazeck FJ. Closing the gap: Solving complex medically relevant genes at scale. medRxiv. 2024 ;.
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. 2024 ;52(4):e18.
Dardas Z, Fatih JM, Jolly A, Dawood M, Du H, Grochowski CM, Jones EG, Jhangiani SN, Wehrens XHT, Liu P, Bi W, Boerwinkle E, Posey JE, Muzny DM, Gibbs RA, Lupski JR, Coban-Akdemir Z, Morris SA. NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy. Genome Med. 2024 ;16(1):53.
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.
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.
Elbendary HM, Marafi D, Saad AK, Elhossini R, Duan R, Rafat K, Jhangiani SN, Gibbs RA, Pehlivan D, Calame DG, Posey JE, Lupski JR, Zaki MS. Novel LSS variants in alopecia and intellectual disability syndrome: New case report and clinical spectrum of LSS-related rare disease traits. Clin Genet. 2023 ;104(3):344-349.
Jolly A, Du H, Borel C, Chen N, Zhao S, Grochowski CM, Duan R, Fatih JM, Dawood M, Salvi S, Jhangiani SN, Muzny DM, Koch A, Rouskas K, Glentis S, Deligeoroglou E, Bacopoulou F, Wise CA, Dietrich JE, Van den Veyver IB, Dimas AS, Brucker S, V Sutton R, Gibbs RA, Antonarakis SE, Wu N, Coban-Akdemir ZH, Zhu L, Posey JE, Lupski JR. Rare variant enrichment analysis supports as a contributory driver gene in the etiology of Mayer-Rokitansky-Küster-Hauser syndrome. HGG Adv. 2023 ;4(3):100188.
2022
Marafi D, Fatih JM, Kaiyrzhanov R, Ferla MP, Gijavanekar C, Al-Maraghi A, Liu N, Sites E, Alsaif HS, Al-Owain M, Zakkariah M, El-Anany E, Guliyeva U, Guliyeva S, Gaba C, Haseeb A, Alhashem AM, Danish E, Karageorgou V, Beetz C, Subhi AA, Mullegama SV, Torti E, Sebastin M, Breilyn MSheck, Duberstein S, Abdel-Hamid MS, Mitani T, Du H, Rosenfeld JA, Jhangiani SN, Akdemir ZCoban, Gibbs RA, Taylor JC, Fakhro KA, Hunter JV, Pehlivan D, Zaki MS, Gleeson JG, Maroofian R, Houlden H, Posey JE, V Sutton R, Alkuraya FS, Elsea SH, Lupski JR. Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy. Brain. 2022 ;145(3):909-924.
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.
Baxter SM, Posey JE, Lake NJ, Sobreira N, Chong JX, Buyske S, Blue EE, Chadwick LH, Coban-Akdemir ZH, Doheny KF, Davis CP, Lek M, Wellington C, Jhangiani SN, Gerstein M, Gibbs RA, Lifton RP, MacArthur DG, Matise TC, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Mane S, Nickerson DA, Rehm HL, O'Donnell-Luria A. Centers for Mendelian Genomics: A decade of facilitating gene discovery. Genet Med. 2022 ;24(4):784-797.
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.
Abdel-Salam GMH, Duan R, Abdel-Hamid MS, Sayed ISM, Jhangiani SN, Khan Z, Du H, Gibbs RA, Posey JE, Marafi D, Lupski JR. Expanding the phenotypic and allelic spectrum of SMG8: Clinical observations reveal overlap with SMG9-associated disease trait. Am J Med Genet A. 2022 ;188(2):648-657.
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.
Forbes LR, Eckstein OS, Gulati N, Peckham-Gregory EC, Ozuah NW, Lubega J, El-Mallawany NK, Agrusa JE, M Poli C, Vogel TP, Chaimowitz NS, Rider NL, Mace EM, Orange JS, Caldwell JW, Aldave-Becerra JC, Jolles S, Saettini F, Chong HJ, Stray-Pedersen A, Heslop HE, Kamdar KY, R Rouce H, Muzny DM, Jhangiani SN, Gibbs RA, Coban-Akdemir ZH, Lupski JR, McClain KL, Allen CE, Chinn IK. Genetic errors of immunity distinguish pediatric nonmalignant lymphoproliferative disorders. J Allergy Clin Immunol. 2022 ;149(2):758-766.
Chander V, Mahmoud M, Hu J, Dardas Z, Grochowski CM, Dawood M, Khayat MM, Li H, Li S, Jhangiani S, Korchina V, Shen H, Weissenberger G, Meng Q, Gingras M-C, Muzny DM, Doddapaneni H, Posey JE, Lupski JR, Sabo A, Murdock DR, Sedlazeck FJ, Gibbs RA. Long read sequencing and expression studies of AHDC1 deletions in Xia-Gibbs syndrome reveal a novel genetic regulatory mechanism. Hum Mutat. 2022 ;43(12):2033-2053.
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.
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.