Publications

Journal Article
Austin-Tse CA, Jobanputra V, Perry DL, Bick D, Taft RJ, Venner E, Gibbs RA, Young T, Barnett S, Belmont JW, Boczek N, Chowdhury S, Ellsworth KA, Guha S, Kulkarni S, Marcou C, Meng L, Murdock DR, Rehman AU, Spiteri E, Thomas-Wilson A, Kearney HM, Rehm HL. Best practices for the interpretation and reporting of clinical whole genome sequencing. NPJ Genom Med. 2022 ;7(1):27.
Richards S, Murali SC. Best Practices in Insect Genome Sequencing: What Works and What Doesn't. Curr Opin Insect Sci. 2015 ;7:1-7.
Johnatty SE, Abdellatif M, Shimmin L, Clark RB, Boerwinkle E. Beta 2 adrenergic receptor 5' haplotypes influence promoter activity. Br J Pharmacol. 2002 ;137(8):1213-6.
D Hallman M, Srinivasan SR, Chen W, Boerwinkle E, Berenson GS. The beta(2)-adrenergic receptor Arg16-gly polymorphism and interactions involving beta(2)- and beta(3)-adrenergic receptor polymorphisms are associated with variations in longitudinal serum lipid profiles: the Bogalusa Heart Study. Metabolism. 2004 ;53(9):1184-91.
Sgourou A, Papachatzopoulou A, Psiouri L, Antoniou M, Zoumbos N, Gibbs RA, Athanassiadou A. The beta-globin C-->G mutation at 6 bp 3' to the termination codon causes beta-thalassaemia by decreasing the mRNA level. Br J Haematol. 2002 ;118(2):671-6.
Poirier C, Ben Hamed S, Garcia-Saldivar P, Kwok SChai, Meguerditchian A, Merchant H, Rogers J, Wells S, Fox AS. Beyond MRI: on the scientific value of combining non-human primate neuroimaging with metadata. Neuroimage. 2021 ;228:117679.
Rogers J, Mahaney MC, Beamer WG, Donahue LR, Rosen CJ. Beyond one gene-one disease: alternative strategies for deciphering genetic determinants of osteoporosis. Calcif Tissue Int. 1997 ;60(3):225-8.
Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: What's next in diagnostic testing for Mendelian conditions. Am J Hum Genet. 2023 ;110(8):1229-1248.
Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: what's next in diagnostic testing for Mendelian conditions. ArXiv. 2023 ;.
Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Karimiani EGhayoor, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JRaza, Ganieva M, Fowler B, Aanicai R, Tayfun GAkay, Saman AAl, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Monajemi GBahrami, Mohammadi P, Samie S, Banu SHusna, Basto JPinto, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Issa AHameed, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CMarques, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha MEugenia, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JKassem, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 2024 ;147(4):1436-1456.
Karaca E, Posey JE, Bostwick B, Liu P, Gezdirici A, Yesil G, Akdemir ZCoban, Bayram Y, Harms FL, Meinecke P, Alawi M, Bacino CA, V Sutton R, Kortüm F, Lupski JR. Biallelic and De Novo Variants in DONSON Reveal a Clinical Spectrum of Cell Cycle-opathies with Microcephaly, Dwarfism and Skeletal Abnormalities. Am J Med Genet A. 2019 ;179(10):2056-2066.
Dworschak GC, Punetha J, Kalanithy JC, Mingardo E, Erdem HB, Akdemir ZC, Karaca E, Mitani T, Marafi D, Fatih JM, Jhangiani SN, Hunter JV, Dakal TChand, Dhabhai B, Dabbagh O, Alsaif HS, Alkuraya FS, Maroofian R, Houlden H, Efthymiou S, Dominik N, Salpietro V, Sultan T, Haider S, Bibi F, Thiele H, Hoefele J, Riedhammer KM, Wagner M, Guella I, Demos M, Keren B, Buratti J, Charles P, Nava C, Héron D, Heide S, Valkanas E, Waddell LB, Jones KJ, Oates EC, Cooper ST, MacArthur D, Syrbe S, Ziegler A, Platzer K, Okur V, Chung WK, O'Shea SA, Alcalay R, Fahn S, Mark PR, Guerrini R, Vetro A, Hudson B, Schnur RE, Hoganson GE, Burton JE, McEntagart M, Lindenberg T, Yilmaz Ö, Odermatt B, Pehlivan D, Posey JE, Lupski JR, Reutter H. Biallelic and monoallelic variants in PLXNA1 are implicated in a novel neurodevelopmental disorder with variable cerebral and eye anomalies. Genet Med. 2021 ;23(9):1715-1725.
Dinckan N, Du R, Akdemir ZC, Bayram Y, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Guven Y, Aktoren O, Kayserili H, Boerwinkle E, Gibbs RA, Posey JE, Lupski JR, Uyguner ZO, Letra A. A biallelic ANTXR1 variant expands the anthrax toxin receptor associated phenotype to tooth agenesis. Am J Med Genet A. 2018 ;176(4):1015-1022.
Punetha J, Karaca E, Gezdirici A, Lamont RE, Pehlivan D, Marafi D, Appendino JP, Hunter JV, Akdemir ZC, Fatih JM, Jhangiani SN, Gibbs RA, A Innes M, Posey JE, Lupski JR. Biallelic CACNA2D2 variants in epileptic encephalopathy and cerebellar atrophy. Ann Clin Transl Neurol. 2019 ;6(8):1395-1406.
Khalaf-Nazzal R, Fasham J, Inskeep KA, Blizzard LE, Leslie JS, Wakeling MN, Ubeyratna N, Mitani T, Griffith JL, Baker W, Al-Hijawi F', Keough KC, Gezdirici A, Pena L, Spaeth CG, Turnpenny PD, Walsh JR, Ray R, Neilson A, Kouranova E, Cui X, Curiel DT, Pehlivan D, Akdemir ZCoban, Posey JE, Lupski JR, Dobyns WB, Stottmann RW, Crosby AH, Baple EL. Bi-allelic CAMSAP1 variants cause a clinically recognizable neuronal migration disorder. Am J Hum Genet. 2022 ;109(11):2068-2079.
Morimoto M, Waller-Evans H, Ammous Z, Song X, Strauss KA, Pehlivan D, Gonzaga-Jauregui C, Puffenberger EG, Holst CR, Karaca E, Brigatti KW, Maguire E, Coban-Akdemir ZH, Amagata A, C Lau C, Chepa-Lotrea X, Macnamara E, Tos T, Isikay S, Nehrebecky M, Overton JD, Klein M, Markello TC, Posey JE, Adams DR, Lloyd-Evans E, Lupski JR, Gahl WA, Malicdan MChristine. Bi-allelic CCDC47 Variants Cause a Disorder Characterized by Woolly Hair, Liver Dysfunction, Dysmorphic Features, and Global Developmental Delay. Am J Hum Genet. 2018 ;103(5):794-807.
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.
Marafi D, Mitani T, Isikay S, Hertecant J, Almannai M, Manickam K, Jamra RAbou, El-Hattab AW, Rajah J, Fatih JM, Du H, Karaca E, Bayram Y, Punetha J, Rosenfeld JA, Jhangiani SN, Boerwinkle E, Akdemir ZC, Erdin S, Hunter JV, Gibbs RA, Pehlivan D, Posey JE, Lupski JR. Biallelic GRM7 variants cause epilepsy, microcephaly, and cerebral atrophy. Ann Clin Transl Neurol. 2020 ;7(5):610-627.
Saad AK, Marafi D, Mitani T, Jolly A, Du H, Elbendary HM, Jhangiani SN, Akdemir ZC, Gibbs RA, Hunter JV, Carvalho CMBC, Pehlivan D, Posey JE, Zaki MS, Lupski JR. Biallelic in-frame deletion in TRAPPC4 in a family with developmental delay and cerebellar atrophy. Brain. 2020 ;143(10):e83.
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.
Ullah E, Lin S, Lu J, Bender C, Webster AR, Malka S, Madhusudhan S, Rees E, Williams D, Agather AR, Cukras CA, Hufnagel RB, Chen R, Huryn LA, Arno G, Guan B. Biallelic Loss-of-Function Variants in UBAP1L and Nonsyndromic Retinal Dystrophies. JAMA Ophthalmol. 2024 ;.
Maroofian R, Kaiyrzhanov R, Cali E, Zamani M, Zaki MS, Ferla M, Tortora D, Sadeghian S, Saadi SMaryam, Abdullah U, Karimiani EGhayoor, Efthymiou S, Yesil G, Alavi S, Shamsi AMAl, Tajsharghi H, Abdel-Hamid MS, Saadi NWaill, Mutairi FAl, Alabdi L, Beetz C, Ali Z, Toosi MBeiraghi, Rudnik-Schöneborn S, Babaei M, Isohanni P, Muhammad J, Khan S, Shalan MAl, Hickey SE, Marom D, Elhanan E, Kurian MA, Marafi D, Saberi A, Hamid M, Spaull R, Meng L, Lalani S, Maqbool S, Rahman F, Seeger J, Palculict TBlake, Lau T, Murphy D, Mencacci NEmanuele, Steindl K, Begemann A, Rauch A, Akbas S, Aslanger ADilruba, Salpietro V, Yousaf H, Ben-Shachar S, Ejeskär K, Aqeel AIAl, High FA, Armstrong-Javors AE, Zahraei SMohammadsa, Seifi T, Zeighami J, Shariati G, Sedaghat A, Asl SNoroozi, Shahrooei M, Zifarelli G, Burglen L, Ravelli C, Zschocke J, Schatz UA, Ghavideldarestani M, Kamel WA, Van Esch H, Hackenberg A, Taylor JC, Al-Gazali L, Bauer P, Gleeson JJ, Alkuraya FSami, Lupski JR, Galehdari H, Azizimalamiri R, Chung WK, Baig SMahmood, Houlden H, Severino M. Biallelic MED27 variants lead to variable ponto-cerebello-lental degeneration with movement disorders. Brain. 2023 ;146(12):5031-5043.
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.
Vetrini F, D'Alessandro LCA, Akdemir ZC, Braxton A, Azamian MS, Eldomery MK, Miller K, Kois C, Sack V, Shur N, Rijhsinghani A, Chandarana J, Ding Y, Holtzman J, Jhangiani SN, Muzny DM, Gibbs RA, Eng CM, Hanchard NA, Harel T, Rosenfeld JA, Belmont JW, Lupski JR, Yang Y. Bi-allelic Mutations in PKD1L1 Are Associated with Laterality Defects in Humans. Am J Hum Genet. 2016 ;99(4):886-893.
Stray-Pedersen A, Cobben J-M, Prescott TE, Lee S, Cang C, Aranda K, Ahmed S, Alders M, Gerstner T, Aslaksen K, Tétreault M, Qin W, Hartley T, Jhangiani SN, Muzny DM, Tarailo-Graovac M, van Karnebeek CDM, Lupski JR, Ren D, Yoon G. Biallelic Mutations in UNC80 Cause Persistent Hypotonia, Encephalopathy, Growth Retardation, and Severe Intellectual Disability. Am J Hum Genet. 2016 ;98(1):202-9.