Selected PUBLICATIONS

 O’Donnell-Luria Lab and Translational Genomics Group authors in bold

* Joint first author

^ Joint second author

# Joint senior author

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection.

Negi S, Stenton SL, Berger SI, Canigiula P, McNulty B, Violich I, Gardner J, Hillaker T, O'Rourke SM, O'Leary MC, Carbonell E, Austin-Tse C, Lemire G, Serrano J, Mangilog B, VanNoy G, Kolmogorov M, Vilain E, O'Donnell-Luria A, Délot E, Miga KH, Monlong J, Paten B.

Am J Hum Genet. 2025 Jan 22. Online ahead of print. 

PMID: 39862869 GREGoR/Broad CMG

Novel Phenotypes and Genotype-Phenotype Correlations in a Large Clinical Cohort of Patients With Kleefstra Syndrome.

Frazier ZJ, Kilic S, Osika H, Mo A, Quinn M, Ballal S, Katz T, Shearer AE, Horlbeck MA, Pais LS, Dies KA, O'Donnell-Luria A, Kossowsky J, Lipton JO, Kleefstra T, Srivastava S.

Clin Genet. 2025 Jan 2. Online ahead of print. 

PMID: 39746677 Clinical/chromatin disorders

Diagnosing missed cases of spinal muscular atrophy in genome, exome, and panel sequencing datasets.

Weisburd B, Sharma R, Pata V, Reimand T, Ganesh VS, Austin-Tse C, Osei-Owusu I, O'Heir E, O'Leary M, Pais L, Stafki SA, Daugherty AL, Folland C, Perić S, Fahmy N, Udd B, Horakova M, Łusakowska A, Manoj R, Nalini A, Karcagi V, Polavarapu K, Lochmüller H, Horvath R, Bönnemann CG, Donkervoort S, Haliloğlu G, Herguner O, Kang PB, Ravenscroft G, Laing N, Scott HS, Töpf A, Straub V, Pajusalu S, Õunap K, Tiao G, Rehm HL, O'Donnell-Luria A.

Genet Med. 2024 Dec 9:101336. Online ahead of print. 

PMID: 39670433 GREGoR/Broad CMG

Neurodevelopmental Disorder Caused by Deletion of CHASERR, a lncRNA Gene.

Ganesh VS*, Riquin K*, Chatron N, Yoon E, Lamar KM, Aziz MC, Monin P, O'Leary MC, Goodrich JK, Garimella KV, England E, Weisburd B, Aguet F, Bacino CA, Murdock DR, Dai H, Rosenfeld JA, Emrick LT, Ketkar S, Sarusi Y, Sanlaville D, Kayani S, Broadbent B, Pengam A, Isidor B, Bezieau S, Cogné B, MacArthur DG, Ulitsky I, Carvill GL#, O'Donnell-Luria A#.

N Engl J Med. 2024 Oct 24;391(16):1511-1518. 

PMID: 39442041 GREGoR/Broad CMG

Leaving no patient behind! Expert recommendation in the use of innovative technologies for diagnosing rare diseases.

van Karnebeek CDM, O'Donnell-Luria A, Baynam G, Baudot A, Groza T, Jans JJM, Lassmann T, Letinturier MCV, Montgomery SB, Robinson PN, Sansen S, Mehrian-Shai R, Steward C, Kosaki K, Durao P, Sadikovic B.

Orphanet J Rare Dis. 2024 Sep 27;19(1):357. Review.

PMID: 39334316  GREGoR

Assessment of the evidence yield for the calibrated PP3/BP4 computational recommendations.

Stenton SL, Pejaver V, Bergquist T, Biesecker LG, Byrne AB, Nadeau EAW, Greenblatt MS, Harrison SM, Tavtigian SV, Radivojac P, Brenner SE, O'Donnell-Luria A; ClinGen Sequence Variant Interpretation Working Group.

Genet Med. 2024 Nov;26(11):101213. 

PMID: 39030733 ClinGen

De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome.

Chen Y, Dawes R^, Kim HC^, Ljungdahl A^, Stenton SL^, Walker S^, Lord J, Lemire G, Martin-Geary AC, Ganesh VS, Ma J, Ellingford JM, Delage E, D'Souza EN, Dong S, Adams DR, Allan K, Bakshi M, Baldwin EE, Berger SI, Bernstein JA, Bhatnagar I, Blair E, Brown NJ, Burrage LC, Chapman K, Coman DJ, Compton AG, Cunningham CA, D'Souza P, Danecek P, Délot EC, Dias KR, Elias ER, Elmslie F, Evans CA, Ewans L, Ezell K, Fraser JL, Gallacher L, Genetti CA, Goriely A, Grant CL, Haack T, Higgs JE, Hinch AG, Hurles ME, Kuechler A, Lachlan KL, Lalani SR, Lecoquierre F, Leitão E, Fevre AL, Leventer RJ, Liebelt JE, Lindsay S, Lockhart PJ, Ma AS, Macnamara EF, Mansour S, Maurer TM, Mendez HR, Metcalfe K, Montgomery SB, Moosajee M, Nassogne MC, Neumann S, O'Donoghue M, O'Leary M, Palmer EE, Pattani N, Phillips J, Pitsava G, Pysar R, Rehm HL, Reuter CM, Revencu N, Riess A, Rius R, Rodan L, Roscioli T, Rosenfeld JA, Sachdev R, Shaw-Smith CJ, Simons C, Sisodiya SM, Snell P, St Clair L, Stark Z, Stewart HS, Tan TY, Tan NB, Temple SEL, Thorburn DR, Tifft CJ, Uebergang E, VanNoy GE, Vasudevan P, Vilain E, Viskochil DH, Wedd L, Wheeler MT, White SM, Wojcik M, Wolfe LA, Wolfenson Z, Wright CF, Xiao C, Zocche D, Rubenstein JL, Markenscoff-Papadimitriou E, Fica SM, Baralle D, Depienne C, MacArthur DG, Howson JMM, Sanders SJ, O'Donnell-Luria A, Whiffin N.

Nature. 2024 Aug;632(8026):832-840. 

PMID: 38991538 GREGoR/Broad CMG

Genome Sequencing for Diagnosing Rare Diseases.

Wojcik MH, Lemire G, Berger E, Zaki MS, Wissmann M, Win W, White SM, Weisburd B, Wieczorek D, Waddell LB, Verboon JM, VanNoy GE, Töpf A, Tan TY, Syrbe S, Strehlow V, Straub V, Stenton SL, Snow H, Singer-Berk M, Silver J, Shril S, Seaby EG, Schneider R, Sankaran VG, Sanchis-Juan A, Russell KA, Reinson K, Ravenscroft G, Radtke M, Popp D, Polster T, Platzer K, Pierce EA, Place EM, Pajusalu S, Pais L, Õunap K, Osei-Owusu I, Opperman H, Okur V, Oja KT, O'Leary M, O'Heir E, Morel CF, Merkenschlager A, Marchant RG, Mangilog BE, Madden JA, MacArthur D, Lovgren A, Lerner-Ellis JP, Lin J, Laing N, Hildebrandt F, Hentschel J, Groopman E, Goodrich J, Gleeson JG, Ghaoui R, Genetti CA, Gburek-Augustat J, Gazda HT, Ganesh VS, Ganapathi M, Gallacher L, Fu JM, Evangelista E, England E, Donkervoort S, DiTroia S, Cooper ST, Chung WK, Christodoulou J, Chao KR, Cato LD, Bujakowska KM, Bryen SJ, Brand H, Bönnemann CG, Beggs AH, Baxter SM, Bartolomaeus T, Agrawal PB, Talkowski M, Austin-Tse C, Abou Jamra R#, Rehm HL#, O'Donnell-Luria A#.

N Engl J Med. 2024 Jun 6;390(21):1985-1997. 

PMID: 38838312 GREGoR/Broad CMG

Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project.

Stenton SL, O'Leary MC, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O'Heir E, Mangilog B, Osei-Owusu I, Pais LS, Serrano J, Singer-Berk M, Weisburd B, Wilson MW, Austin-Tse C, Abdelhakim M, Althagafi A, Babbi G, Bellazzi R, Bovo S, Carta MG, Casadio R, Coenen PJ, De Paoli F, Floris M, Gajapathy M, Hoehndorf R, Jacobsen JOB, Joseph T, Kamandula A, Katsonis P, Kint C, Lichtarge O, Limongelli I, Lu Y, Magni P, Mamidi TKK, Martelli PL, Mulargia M, Nicora G, Nykamp K, Pejaver V, Peng Y, Pham THC, Podda MS, Rao A, Rizzo E, Saipradeep VG, Savojardo C, Schols P, Shen Y, Sivadasan N, Smedley D, Soru D, Srinivasan R, Sun Y, Sunderam U, Tan W, Tiwari N, Wang X, Wang Y, Williams A, Worthey EA, Yin R, You Y, Zeiberg D, Zucca S, Bakolitsa C, Brenner SE, Fullerton SM, Radivojac P, Rehm HL, O'Donnell-Luria A.

Hum Genomics. 2024 Apr 29;18(1):44. 

PMID: 38685113 CAGI

KMT2E-Related Neurodevelopmental Disorder.

Pais L, Rodan L, O'Donnell-Luria A.

2024 Apr 18. GeneReviews®. Review.

PMID: 38648332 Clinical/chromatin disorders

Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease.

Lemire G*, Sanchis-Juan A*, Russell K, Baxter S, Chao KR, Singer-Berk M, Groopman E, Wong I, England E, Goodrich J, Pais L, Austin-Tse C, DiTroia S, O'Heir E, Ganesh VS, Wojcik MH, Evangelista E, Snow H, Osei-Owusu I, Fu J, Singh M, Mostovoy Y, Huang S, Garimella K, Kirkham SL, Neil JE, Shao DD, Walsh CA, Argilli E, Le C, Sherr EH, Gleeson JG, Shril S, Schneider R, Hildebrandt F, Sankaran VG, Madden JA, Genetti CA, Beggs AH, Agrawal PB, Bujakowska KM, Place E, Pierce EA, Donkervoort S, Bönnemann CG, Gallacher L, Stark Z, Tan TY, White SM, Töpf A, Straub V, Fleming MD, Pollak MR, Õunap K, Pajusalu S, Donald KA, Bruwer Z, Ravenscroft G, Laing NG, MacArthur DG, Rehm HL, Talkowski ME, Brand H#, O'Donnell-Luria A#.

Am J Hum Genet. 2024 May 2;111(5):863-876. 

PMID: 38565148 GREGoR/Broad CMG

Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort.

Dias KR, Shrestha R, Schofield D, Evans CA, O'Heir E, Zhu Y, Zhang F, Standen K, Weisburd B, Stenton SL, Sanchis-Juan A, Brand H, Talkowski ME, Ma A, Ghedia S, Wilson M, Sandaradura SA, Smith J, Kamien B, Turner A, Bakshi M, Adès LC, Mowat D, Regan M, McGillivray G, Savarirayan R, White SM, Tan TY, Stark Z, Brown NJ, Pérez-Jurado LA, Krzesinski E, Hunter MF, Akesson L, Fennell AP, Yeung A, Boughtwood T, Ewans LJ, Kerkhof J, Lucas C, Carey L, French H, Rapadas M, Stevanovski I, Deveson IW, Cliffe C, Elakis G, Kirk EP, Dudding-Byth T, Fletcher J, Walsh R, Corbett MA, Kroes T, Gecz J, Meldrum C, Cliffe S, Wall M, Lunke S, North K, Amor DJ, Field M, Sadikovic B, Buckley MF, O'Donnell-Luria A, Roscioli T.

Genet Med. 2024 May;26(5):101076. 

PMID: 38258669 GREGoR/Broad CMG

A gene pathogenicity tool "GenePy" identifies missed biallelic diagnoses in the 100,000 Genomes Project.

Seaby EG, Leggatt G, Cheng G, Thomas NS, Ashton JJ, Stafford I, Baralle D, Rehm HL, O'Donnell-Luria A, Ennis S; Genomics England Research Consortium.

Genet Med. 2024 Apr;26(4):101073. 

PMID: 38245859 GREGoR/Broad CMG

Inferring compound heterozygosity from large-scale exome sequencing data.

Guo MH*, Francioli LC*, Stenton SL, Goodrich JK, Watts NA, Singer-Berk M, Groopman E, Darnowsky PW, Solomonson M, Baxter S; gnomAD Project Consortium; Tiao G, Neale BM, Hirschhorn JN, Rehm HL, Daly MJ, O'Donnell-Luria A, Karczewski KJ, MacArthur DG, Samocha KE.

Nat Genet. 2024 Jan;56(1):152-161. 

PMID: 38057443 gnomAD

Advanced variant classification framework reduces the false positive rate of predicted loss-of-function variants in population sequencing data.

Singer-Berk M*, Gudmundsson S*, Baxter S, Seaby EG, England E, Wood JC, Son RG, Watts NA, Karczewski KJ, Harrison SM, MacArthur DG, Rehm HL, O'Donnell-Luria A.

Am J Hum Genet. 2023 Sep 7;110(9):1496-1508. 

PMID: 37633279 gnomAD

Beyond the exome: What's next in diagnostic testing for Mendelian conditions.

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; Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium; Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE.

Am J Hum Genet. 2023 Aug 3;110(8):1229-1248. Review.

PMID: 37541186 GREGoR

Phenotype and genetic analysis of data collected within the first year of NeuroDev.

Kipkemoi P, Kim HA, Christ B, O'Heir E, Allen J, Austin-Tse C, Baxter S, Brand H, Bryant S, Buser N, de Menil V, Eastman E, Murugasen S, Galvin A, Kombe M, Ngombo A, Mkubwa B, Mwangi P, Kipkoech C, Lovgren A, MacArthur DG, Melly B, Mwangasha K, Martin A, Nkambule LL, Sanchis-Juan A, Singer-Berk M, Talkowski ME, VanNoy G, van der Merwe C; NeuroDev Project; Newton C, O'Donnell-Luria A, Abubakar A#, Donald KA#, Robinson EB#.

Neuron. 2023 Sep 20;111(18):2800-2810.e5. 

PMID: 37463579 NeuroDev project

First-Tier Next Generation Sequencing for Newborn Screening: An Important Role for Biochemical Second-Tier Testing.

Stenton SL, Campagna M, Philippakis A, O'Donnell-Luria A, Gelb MH.

Genet Med Open. 2023;1(1):100821. 

PMID: 39238532 Prevalence

Targeting de novo loss-of-function variants in constrained disease genes improves diagnostic rates in the 100,000 Genomes Project.

Seaby EG, Thomas NS, Webb A, Brittain H, Taylor Tavares AL; Genomics England Consortium; Baralle D, Rehm HL, O'Donnell-Luria A#, Ennis S#.

Hum Genet. 2023 Mar;142(3):351-362. 

PMID: 36477409 GREGoR/Broad CMG

seqr: A web-based analysis and collaboration tool for rare disease genomics.

Pais LS, Snow H, Weisburd B, Zhang S, Baxter SM, DiTroia S, O'Heir E, England E, Chao KR, Lemire G, Osei-Owusu I, VanNoy GE, Wilson M, Nguyen K, Arachchi H, Phu W, Solomonson M, Mano S, O'Leary M, Lovgren A, Babb L, Austin-Tse CA, Rehm HL, MacArthur DG, O'Donnell-Luria A.

Hum Mutat. 2022 Jun;43(6):698-707. 

PMID: 35266241 GREGoR/Broad CMG

Centers for Mendelian Genomics: A decade of facilitating gene discovery.

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; Centers for Mendelian Genomics Consortium; Rehm HL#, O'Donnell-Luria A#.

Genet Med. 2022 Apr;24(4):784-797. Review.

PMID: 35148959  Broad CMG

Variant interpretation using population databases: Lessons from gnomAD.

Gudmundsson S, Singer-Berk M, Watts NA, Phu W, Goodrich JK, Solomonson M; Genome Aggregation Database Consortium; Rehm HL, MacArthur DG, O'Donnell-Luria A.

Hum Mutat. 2022 Aug;43(8):1012-1030. Review.

PMID: 34859531 gnomAD

Strategies to Uplift Novel Mendelian Gene Discovery for Improved Clinical Outcomes.

Seaby EG, Rehm HL, O'Donnell-Luria A.

Front Genet. 2021 Jun 17;12:674295. Review.

PMID: 34220947 Broad CMG

Comprehensive analysis of ADA2 genetic variants and estimation of carrier frequency driven by a function-based approach.

Jee H, Huang Z, Baxter S, Huang Y, Taylor ML, Henderson LA, Rosenzweig S, Sharma A, Chambers EP, Hershfield MS, Zhou Q, Dedeoglu F, Aksentijevich I, Nigrovic PA, O'Donnell-Luria A, Lee PY.

J Allergy Clin Immunol. 2022 Jan;149(1):379-387. 

PMID: 34004258 Prevalence

Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome.

Dyment DA*, O'Donnell-Luria A*, Agrawal PB, Coban Akdemir Z, Aleck KA, Antaki D, Al Sharhan H, Au PB, Aydin H, Beggs AH, Bilguvar K, Boerwinkle E, Brand H, Brownstein CA, Buyske S, Chodirker B, Choi J, Chudley AE, Clericuzio CL, Cox GF, Curry C, de Boer E, de Vries BBA, Dunn K, Dutmer CM, England EM, Fahrner JA, Geckinli BB, Genetti CA, Gezdirici A, Gibson WT, Gleeson JG, Greenberg CR, Hall A, Hamosh A, Hartley T, Jhangiani SN, Karaca E, Kernohan K, Lauzon JL, Lewis MES, Lowry RB, López-Giráldez F, Matise TC, McEvoy-Venneri J, McInnes B, Mhanni A, Garcia Minaur S, Moilanen J, Nguyen A, Nowaczyk MJM, Posey JE, Õunap K, Pehlivan D, Pajusalu S, Penney LS, Poterba T, Prontera P, Doriqui MJR, Sawyer SL, Sobreira N, Stanley V, Torun D, Wargowski D, Witmer PD, Wong I, Xing J, Zaki MS, Zhang Y; Care4Rare Consortium; Centers for Mendelian Genomics; Boycott KM, Bamshad MJ, Nickerson DA, Blue EE#, Innes AM#.

Am J Med Genet A. 2021 Jan;185(1):119-133. 

PMID: 33098347 Broad CMG

Characterization of Prevalence and Health Consequences of Uniparental Disomy in Four Million Individuals from the General Population.

Nakka P, Pattillo Smith S, O'Donnell-Luria AH, McManus KF; 23andMe Research Team; Mountain JL, Ramachandran S, Sathirapongsasuti JF.

Am J Hum Genet. 2019 Nov 7;105(5):921-932. 

PMID: 31607426 Prevalence

Improving the Understanding of Genetic Variants in Rare Disease With Large-scale Reference Populations.

Whiffin N, Ware JS, O'Donnell-Luria A.

JAMA. 2019 Oct 1;322(13):1305-1306. 

PMID: 31469401 gnomAD

Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy.

O'Donnell-Luria AH, Pais LS, Faundes V, Wood JC, Sveden A, Luria V, Abou Jamra R, Accogli A, Amburgey K, Anderlid BM, Azzarello-Burri S, Basinger AA, Bianchini C, Bird LM, Buchert R, Carre W, Ceulemans S, Charles P, Cox H, Culliton L, Currò A; Deciphering Developmental Disorders (DDD) Study; Demurger F, Dowling JJ, Duban-Bedu B, Dubourg C, Eiset SE, Escobar LF, Ferrarini A, Haack TB, Hashim M, Heide S, Helbig KL, Helbig I, Heredia R, Héron D, Isidor B, Jonasson AR, Joset P, Keren B, Kok F, Kroes HY, Lavillaureix A, Lu X, Maas SM, Maegawa GHB, Marcelis CLM, Mark PR, Masruha MR, McLaughlin HM, McWalter K, Melchinger EU, Mercimek-Andrews S, Nava C, Pendziwiat M, Person R, Ramelli GP, Ramos LLP, Rauch A, Reavey C, Renieri A, Rieß A, Sanchez-Valle A, Sattar S, Saunders C, Schwarz N, Smol T, Srour M, Steindl K, Syrbe S, Taylor JC, Telegrafi A, Thiffault I, Trauner DA, van der Linden H Jr, van Koningsbruggen S, Villard L, Vogel I, Vogt J, Weber YG, Wentzensen IM, Widjaja E, Zak J, Baxter S, Banka S, Rodan LH.

Am J Hum Genet. 2019 Jun 6;104(6):1210-1222. 

PMID: 31079897 Clinical/chromatin disorders/Broad CMG

Pathogenic ASXL1 somatic variants in reference databases complicate germline variant interpretation for Bohring-Opitz Syndrome.

Carlston CM*, O'Donnell-Luria AH*, Underhill HR, Cummings BB, Weisburd B, Minikel EV, Birnbaum DP; Exome Aggregation Consortium; Tvrdik T, MacArthur DG, Mao R.

Hum Mutat. 2017 May;38(5):517-523. 

PMID: 28229513 gnomAD

A Clinician's perspective on clinical exome sequencing.

O'Donnell-Luria AH, Miller DT.

Hum Genet. 2016 Jun;135(6):643-54. Review.

PMID: 27126233 Clinical