Deciphering Developmental Disorders (DDD)

The Deciphering Developmental Disorders (DDD) study is a research collaboration between the Wellcome Trust Sanger Institute, the NHS clinical genetics services and families across the UK and Ireland. The project aims to improve the diagnosis of children with developmental disorders by using high-resolution microarray and massively parallel sequencing technologies on 12,000 children and their parents. Genetic changes that explain the child's symptoms will be displayed in the DECIPHER database (https://decipher.sanger.ac.uk). Extended datasets generated by the DDD project will be available in the European Genome-Phenome Archive with access carefully managed by a Data Access Committee.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

26 Datasets 48 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001001114	DDD DATAFREEZE 2013-12-18: 1133 trios - exome sequence BAM files (Ref: DDD Nature 2015)		-
EGAD00001001355	DDD DATAFREEZE 2013-12-18: 1133 trios - VCF files (Ref: DDD Nature 2015)		-
EGAD00001001413	DDD DATAFREEZE 2013-12-18: 1133 trios - README, family trios, phenotypes, validated DNMs (Ref: DDD Nature 2015)		-
EGAD00001001848	DDD DATAFREEZE 2014-11-04: 4293 trios - VCF files		-
EGAD00001001977	DDD DATAFREEZE 2014-11-04: 4293 trios - phenotypic and family descriptions		-
EGAD00001002748	DDD DATAFREEZE 2014-11-04: 4293 trios - exome sequence CRAM files		-
EGAD00001003340	DDD DATAFREEZE 2016-10-03: 7831 trios - VCF files		-
EGAD00001003350	DDD DATAFREEZE 2016-10-03: 7831 trios - phenotypic and family descriptions		-
EGAD00001003406	DDD DATAFREEZE 2016-10-03: 7831 trios - exome sequence CRAM files		-
EGAD00001004388	DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - phenotypic and family descriptions		-
EGAD00001004389	DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence VCF files		-
EGAD00001004390	DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence CRAM files		-
EGAD00001004586	Variants and WGS data for Gardner et al. 2018 (biorxiv 471375). One VCF each for Alu, L1, and SVA. Flat text file and WGS for processed pseudogenes.	HiSeq X Ten	-
EGAD00001005728	aCGH CNV detection by CNsolidate for 6,827 DDD probands		-
EGAD00001008497	CRAM files and VCF for DDD_1 and their parents. Also de novo mutations file for hypermutated DDD_1 child as described in the manuscript ‘Genetic and chemotherapeutic influences of germline hypermutation’ by Kaplanis et al. which will be published in Nature shortly.	HiSeq X Ten	3
EGAD00001010136	DDD resource files (e.g. link between sample and individual ids)		-
EGAD00001010137	Candidate diagnostic variants reported into DECIPHER by 4 April 2022, annotated with clinical and automated pathogenicity assertions (see DOI: 10.1056/NEJMoa2209046). Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland, Wright et al, NEJM 2023.		-
EGAD00010000702	SNP-chip genotyping data for one proband in the DDD study (Ref : Carvalho AJHG 2015)		1
EGAD00010001598	Batch 1 of unfiltered genotype data for DDD Study patients (N=2,997), some of which were used in the neurodevelopmental disorder discovery GWAS (Niemi et al., Nature 2018). Samples were genotyped on the Illumina HumanCoreExome BeadChip. QC'd data is available in release EGAD00010001604	Illumina HumanCoreExome-24v1-0	3000
EGAD00010001600	Batch 2 of unfiltered genotype for DDD Study patients (N=8,286), some of which were used in the neurodevelopmental disorder discovery GWAS (Niemi et al., Nature 2018). Samples were genotyped on the Illumina InfiniumCoreExome Beadchip. QC'd data is available in release EGAD00010001604	Illumina HumanCoreExome-24v1-1	8207
EGAD00010001602	Unfiltered genotype data for DDD Study trios (patient and parents) (N=2,166 samples), some of which were used for replication of neurodevelopmental disorder polygenic risk (Niemi et al., Nature 2018). Samples were genotyped on the Illumina HumanOmniExpress BeadChip	Illumina SangerDDD_OmniExPlusv1_15019773	3822
EGAD00010001604	Post-QC (pre-imputation) genotype data for N=6,983 DDD probands included in the neurodevelopmental disorder discovery GWAS (Niemi et al., Nature 2018). Consists of filtered set of samples and variants from EGAD00010001598 and EGAD00010001600. Includes patient HPO phenotype terms and GWAS summary statistics (including imputed variants). Samples were genotyped on the Illumina HumanCoreExome BeadChip and Illumina InfiniumCoreExome Beadchip	Illumina HumanCoreExome-24v1	6987
EGAD00010001606	Post-QC (pre-imputation) genotype data for N=2,166, a subset of trios described in EGAD00010001602. These data form N=722 complete trios in which the proband has a neurodevelopmental phenotype (Niemi et al. Nature 2018). Includes HPO phenotype terms for patients. Samples were genotyped on the Illumina HumanOmniExpress BeadChip	Illumina SangerDDD_OmniExPlusv1_15019773 MiSeq	2225
EGAD00010002567	Unfiltered genotype data for a pilot study (Batch 1) of 1,140 DDD Study participants (and 12 "Empty" samples). Samples include 380 mothers, 382 fathers and 378 probands, and form 376 trios. Most of the probands have been previously genoyped on the llumina HumanCoreExome BeadChip (EGAD00010001598) or the Illumina InfiniumCoreExome Beadchip (EGAD00010001600). All samples were genotyped on the Illumina Global Screening Array.	Illumina Global Screening Array	1140
EGAD00010002568	QC-ed data of 9,534 DDD Study participants, including 8,879 individuals with inferred GBR ancestry. Details of genotype QC can be found in https://www.medrxiv.org/content/10.1101/2023.04.20.23288860v1.full.pdf. Genome builds are indicated in the file name. Related individuals have not been removed. Of the 9,534 samples there are 3,148 mothers, 3,138 fathers and 3,248 probands, which form 3,099 trios. Of the 8,879 GBR samples, there are 2,931 mothers, 2,937 father and 3,011 probands, which form 2,788 trios. Most of the probands have been previously genoyped on the llumina HumanCoreExome BeadChip (EGAD00010001598) or the Illumina InfiniumCoreExome Beadchip (EGAD00010001600). All samples were genotyped on the Illumina Global Screening Array.	Illumina Global Screening Array	9534
EGAD00010002569	Unfiltered genotype data for a larger batch (Batch 2) of 8,697 DDD Study participants (and 1 "Blank" sample). Samples include 2,858 mothers, 2,857 fathers and 2,982 probands, and form 2,918 trios. Most of the probands have been previously genoyped on the llumina HumanCoreExome BeadChip (EGAD00010001598) or the Illumina InfiniumCoreExome Beadchip (EGAD00010001600). All samples were genotyped on the Illumina Global Screening Array.	Illumina Global Screening Array	9846

Publications	Citations
Large-scale discovery of novel genetic causes of developmental disorders. Deciphering Developmental Disorders Study. Nature 519: 2015 223-228	667
Absence of heterozygosity due to template switching during replicative rearrangements. Carvalho CM, Pfundt R, King DA, Lindsay SJ, Zuccherato LW, Macville MV, Liu P, Johnson D, Stankiewicz P, Brown CW, DDD Study, Shaw CA, Hurles ME, Ira G, Hastings PJ, Brunner HG, Lupski JR. Am J Hum Genet 96: 2015 555-564	36
B56δ-related protein phosphatase 2A dysfunction identified in patients with intellectual disability. Houge G, Haesen D, Vissers LE, Mehta S, Parker MJ, Wright M, Vogt J, McKee S, Tolmie JL, Cordeiro N, Kleefstra T, Willemsen MH, Reijnders MR, Berland S, Hayman E, Lahat E, Brilstra EH, van Gassen KL, Zonneveld-Huijssoon E, de Bie CI, Hoischen A, Eichler EE, Holdhus R, Steen VM, Døskeland SO, Hurles ME, FitzPatrick DR, Janssens V. J Clin Invest 125: 2015 3051-3062	63
Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families. Akawi N, McRae J, Ansari M, Balasubramanian M, Blyth M, Brady AF, Clayton S, Cole T, Deshpande C, Fitzgerald TW, Foulds N, Francis R, Gabriel G, Gerety SS, Goodship J, Hobson E, Jones WD, Joss S, King D, Klena N, Kumar A, Lees M, Lelliott C, Lord J, McMullan D, O'Regan M, Osio D, Piombo V, Prigmore E, Rajan D, Rosser E, Sifrim A, Smith A, Swaminathan GJ, Turnpenny P, Whitworth J, Wright CF, Firth HV, Barrett JC, Lo CW, FitzPatrick DR, Hurles ME, DDD study. Nat Genet 47: 2015 1363-1369	97
Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders. Singh T, Kurki MI, Curtis D, Purcell SM, Crooks L, McRae J, Suvisaari J, Chheda H, Blackwood D, Breen G, Pietiläinen O, Gerety SS, Ayub M, Blyth M, Cole T, Collier D, Coomber EL, Craddock N, Daly MJ, Danesh J, DiForti M, Foster A, Freimer NB, Geschwind D, Johnstone M, Joss S, Kirov G, Körkkö J, Kuismin O, Holmans P, Hultman CM, Iyegbe C, Lönnqvist J, Männikkö M, McCarroll SA, McGuffin P, McIntosh AM, McQuillin A, Moilanen JS, Moore C, Murray RM, Newbury-Ecob R, Ouwehand W, Paunio T, Prigmore E, Rees E, Roberts D, Sambrook J, Sklar P, St Clair D, Veijola J, Walters JT, Williams H, Swedish Schizophrenia Study, INTERVAL Study, DDD Study, UK10 K Consortium, Sullivan PF, Hurles ME, O'Donovan MC, Palotie A, Owen MJ, Barrett JC. Nat Neurosci 19: 2016 571-577	249
BCL11A Haploinsufficiency Causes an Intellectual Disability Syndrome and Dysregulates Transcription. Dias C, Estruch SB, Graham SA, McRae J, Sawiak SJ, Hurst JA, Joss SK, Holder SE, Morton JE, Turner C, Thevenon J, Mellul K, Sánchez-Andrade G, Ibarra-Soria X, Deriziotis P, Santos RF, Lee SC, Faivre L, Kleefstra T, Liu P, Hurles ME, DDD Study, Fisher SE, Logan DW. Am J Hum Genet 99: 2016 253-274	90
Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing. Sifrim A, Hitz MP, Wilsdon A, Breckpot J, Turki SH, Thienpont B, McRae J, Fitzgerald TW, Singh T, Swaminathan GJ, Prigmore E, Rajan D, Abdul-Khaliq H, Banka S, Bauer UM, Bentham J, Berger F, Bhattacharya S, Bu'Lock F, Canham N, Colgiu IG, Cosgrove C, Cox H, Daehnert I, Daly A, Danesh J, Fryer A, Gewillig M, Hobson E, Hoff K, Homfray T, INTERVAL Study, Kahlert AK, Ketley A, Kramer HH, Lachlan K, Lampe AK, Louw JJ, Manickara AK, Manase D, McCarthy KP, Metcalfe K, Moore C, Newbury-Ecob R, Omer SO, Ouwehand WH, Park SM, Parker MJ, Pickardt T, Pollard MO, Robert L, Roberts DJ, Sambrook J, Setchfield K, Stiller B, Thornborough C, Toka O, Watkins H, Williams D, Wright M, Mital S, Daubeney PE, Keavney B, Goodship J, UK10K Consortium, Abu-Sulaiman RM, Klaassen S, Wright CF, Firth HV, Barrett JC, Devriendt K, FitzPatrick DR, Brook JD, Deciphering Developmental Disorders Study, Hurles ME. Nat Genet 48: 2016 1060-1065	231
Biallelic Variants in UBA5 Link Dysfunctional UFM1 Ubiquitin-like Modifier Pathway to Severe Infantile-Onset Encephalopathy. Muona M, Ishimura R, Laari A, Ichimura Y, Linnankivi T, Keski-Filppula R, Herva R, Rantala H, Paetau A, Pöyhönen M, Obata M, Uemura T, Karhu T, Bizen N, Takebayashi H, McKee S, Parker MJ, Akawi N, McRae J, Hurles ME, DDD Study, Kuismin O, Kurki MI, Anttonen AK, Tanaka K, Palotie A, Waguri S, Lehesjoki AE, Komatsu M. Am J Hum Genet 99: 2016 683-694	53
Mutations in the HECT domain of NEDD4L lead to AKT-mTOR pathway deregulation and cause periventricular nodular heterotopia. Broix L, Jagline H, Ivanova E, Schmucker S, Drouot N, Clayton-Smith J, Pagnamenta AT, Metcalfe KA, Isidor B, Louvier UW, Poduri A, Taylor JC, Tilly P, Poirier K, Saillour Y, Lebrun N, Stemmelen T, Rudolf G, Muraca G, Saintpierre B, Elmorjani A, Deciphering Developmental Disorders study, Moïse M, Weirauch NB, Guerrini R, Boland A, Olaso R, Masson C, Tripathy R, Keays D, Beldjord C, Nguyen L, Godin J, Kini U, Nischké P, Deleuze JF, Bahi-Buisson N, Sumara I, Hinckelmann MV, Chelly J. Nat Genet 48: 2016 1349-1358	60
Prevalence and architecture of de novo mutations in developmental disorders. Deciphering Developmental Disorders Study. Nature 542: 2017 433-438	763
Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders. Pagnamenta AT, Murakami Y, Taylor JM, Anzilotti C, Howard MF, Miller V, Johnson DS, Tadros S, Mansour S, Temple IK, Firth R, Rosser E, Harrison RE, Kerr B, Popitsch N, DDD Study, Kinoshita T, Taylor JC, Kini U. Eur J Hum Genet 25: 2017 669-679	45
Detection of structural mosaicism from targeted and whole-genome sequencing data. King DA, Sifrim A, Fitzgerald TW, Rahbari R, Hobson E, Homfray T, Mansour S, Mehta SG, Shehla M, Tomkins SE, Vasudevan PC, Hurles ME, Deciphering Developmental Disorders Study. Genome Res 27: 2017 1704-1714	36
De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability. Küry S, van Woerden GM, Besnard T, Proietti Onori M, Latypova X, Towne MC, Cho MT, Prescott TE, Ploeg MA, Sanders S, Stessman HAF, Pujol A, Distel B, Robak LA, Bernstein JA, Denommé-Pichon AS, Lesca G, Sellars EA, Berg J, Carré W, Busk ØL, van Bon BWM, Waugh JL, Deardorff M, Hoganson GE, Bosanko KB, Johnson DS, Dabir T, Holla ØL, Sarkar A, Tveten K, de Bellescize J, Braathen GJ, Terhal PA, Grange DK, van Haeringen A, Lam C, Mirzaa G, Burton J, Bhoj EJ, Douglas J, Santani AB, Nesbitt AI, Helbig KL, Andrews MV, Begtrup A, Tang S, van Gassen KLI, Juusola J, Foss K, Enns GM, Moog U, Hinderhofer K, Paramasivam N, Lincoln S, Kusako BH, Lindenbaum P, Charpentier E, Nowak CB, Cherot E, Simonet T, Ruivenkamp CAL, Hahn S, Brownstein CA, Xia F, Schmitt S, Deb W, Bonneau D, Nizon M, Quinquis D, Chelly J, Rudolf G, Sanlaville D, Parent P, Gilbert-Dussardier B, Toutain A, Sutton VR, Thies J, Peart-Vissers LELM, Boisseau P, Vincent M, Grabrucker AM, Dubourg C, Undiagnosed Diseases Network, Tan WH, Verbeek NE, Granzow M, Santen GWE, Shendure J, Isidor B, Pasquier L, Redon R, Yang Y, State MW, Kleefstra T, Cogné B, GEM HUGO, Deciphering Developmental Disorders Study, Petrovski S, Retterer K, Eichler EE, Rosenfeld JA, Agrawal PB, Bézieau S, Odent S, Elgersma Y, Mercier S. Am J Hum Genet 101: 2017 768-788	84
BRD4 interacts with NIPBL and BRD4 is mutated in a Cornelia de Lange-like syndrome. Olley G, Ansari M, Bengani H, Grimes GR, Rhodes J, von Kriegsheim A, Blatnik A, Stewart FJ, Wakeling E, Carroll N, Ross A, Park SM, Deciphering Developmental Disorders Study, Bickmore WA, Pradeepa MM, FitzPatrick DR. Nat Genet 50: 2018 329-332	71
De novo mutations in regulatory elements in neurodevelopmental disorders. Short PJ, McRae JF, Gallone G, Sifrim A, Won H, Geschwind DH, Wright CF, Firth HV, FitzPatrick DR, Barrett JC, Hurles ME. Nature 555: 2018 611-616	135
Common genetic variants contribute to risk of rare severe neurodevelopmental disorders. Niemi MEK, Martin HC, Rice DL, Gallone G, Gordon S, Kelemen M, McAloney K, McRae J, Radford EJ, Yu S, Gecz J, Martin NG, Wright CF, Fitzpatrick DR, Firth HV, Hurles ME, Barrett JC. Nature 562: 2018 268-271	162
Quantifying the contribution of recessive coding variation to developmental disorders. Martin HC, Jones WD, McIntyre R, Sanchez-Andrade G, Sanderson M, Stephenson JD, Jones CP, Handsaker J, Gallone G, Bruntraeger M, McRae JF, Prigmore E, Short P, Niemi M, Kaplanis J, Radford EJ, Radford EJ, Akawi N, Balasubramanian M, Dean J, Horton R, Hulbert A, Johnson DS, Johnson K, Kumar D, Lynch SA, Mehta SG, Morton J, Parker MJ, Splitt M, Turnpenny PD, Vasudevan PC, Wright M, Bassett A, Gerety SS, Wright CF, FitzPatrick DR, Firth HV, Hurles ME, Barrett JC, Deciphering Developmental Disorders Study. Science 362: 2018 1161-1164	96
Pathogenicity and selective constraint on variation near splice sites. Lord J, Gallone G, Short PJ, McRae JF, Ironfield H, Wynn EH, Gerety SS, He L, Kerr B, Johnson DS, McCann E, Kinning E, Flinter F, Temple IK, Clayton-Smith J, McEntagart M, Lynch SA, Joss S, Douzgou S, Dabir T, Clowes V, McConnell VPM, Lam W, Wright CF, FitzPatrick DR, Firth HV, Barrett JC, Hurles ME, Deciphering Developmental Disorders study. Genome Res 29: 2019 159-170	45
Delineation of dominant and recessive forms of LZTR1-associated Noonan syndrome. Pagnamenta AT, Kaisaki PJ, Bennett F, Burkitt-Wright E, Martin HC, Ferla MP, Taylor JM, Gompertz L, Lahiri N, Tatton-Brown K, Newbury-Ecob R, Henderson A, Joss S, Weber A, Carmichael J, Turnpenny PD, McKee S, Forzano F, Ashraf T, Bradbury K, Shears D, Kini U, de Burca A, DDD Study, Blair E, Taylor JC, Stewart H. Clin Genet 95: 2019 693-703	25
Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP. Thormann A, Halachev M, McLaren W, Moore DJ, Svinti V, Campbell A, Kerr SM, Tischkowitz M, Hunt SE, Dunlop MG, Hurles ME, Wright CF, Firth HV, Cunningham F, FitzPatrick DR. Nat Commun 10: 2019 2373	66
Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations. Kaplanis J, Akawi N, Gallone G, McRae JF, Prigmore E, Wright CF, Fitzpatrick DR, Firth HV, Barrett JC, Hurles ME, Deciphering Developmental Disorders study. Genome Res 29: 2019 1047-1056	26
Clinically-relevant postzygotic mosaicism in parents and children with developmental disorders in trio exome sequencing data. Wright CF, Prigmore E, Rajan D, Handsaker J, McRae J, Kaplanis J, Fitzgerald TW, FitzPatrick DR, Firth HV, Hurles ME. Nat Commun 10: 2019 2985	41
AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature. Birgmeier J, Deisseroth CA, Hayward LE, Galhardo LMT, Tierno AP, Jagadeesh KA, Stenson PD, Cooper DN, Bernstein JA, Haeussler M, Bejerano G. Genet Med 22: 2020 362-370	14
Contribution of retrotransposition to developmental disorders. Gardner EJ, Prigmore E, Gallone G, Danecek P, Samocha KE, Handsaker J, Gerety SS, Ironfield H, Short PJ, Sifrim A, Singh T, Chandler KE, Clement E, Lachlan KL, Prescott K, Rosser E, FitzPatrick DR, Firth HV, Hurles ME. Nat Commun 10: 2019 4630	36
GTX.Digest.VCF: an online NGS data interpretation system based on intelligent gene ranking and large-scale text mining. Jiang Y, Wu C, Zhang Y, Zhang S, Yu S, Lei P, Lu Q, Xi Y, Wang H, Song Z. BMC Med Genomics 12: 2019 193	4
AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature. Birgmeier J, Haeussler M, Deisseroth CA, Steinberg EH, Jagadeesh KA, Ratner AJ, Guturu H, Wenger AM, Diekhans ME, Stenson PD, Cooper DN, Ré C, Beggs AH, Bernstein JA, Bejerano G. Sci Transl Med 12: 2020 eaau9113	42
SLC12A2 variants cause a neurodevelopmental disorder or cochleovestibular defect. McNeill A, Iovino E, Mansard L, Vache C, Baux D, Bedoukian E, Cox H, Dean J, Goudie D, Kumar A, Newbury-Ecob R, Fallerini C, Renieri A, Lopergolo D, Mari F, Blanchet C, Willems M, Roux AF, Pippucci T, Delpire E. Brain 143: 2020 2380-2387	30
Evidence for 28 genetic disorders discovered by combining healthcare and research data. Kaplanis J, Samocha KE, Wiel L, Zhang Z, Arvai KJ, Eberhardt RY, Gallone G, Lelieveld SH, Martin HC, McRae JF, Short PJ, Torene RI, de Boer E, Danecek P, Gardner EJ, Huang N, Lord J, Martincorena I, Pfundt R, Reijnders MRF, Yeung A, Yntema HG, Deciphering Developmental Disorders Study, Vissers LELM, Juusola J, Wright CF, Brunner HG, Firth HV, FitzPatrick DR, Barrett JC, Hurles ME, Gilissen C, Retterer K. Nature 586: 2020 757-762	258
Missense variants in the N-terminal domain of the A isoform of FHF2/FGF13 cause an X-linked developmental and epileptic encephalopathy. Fry AE, Marra C, Derrick AV, Pickrell WO, Higgins AT, Te Water Naude J, McClatchey MA, Davies SJ, Metcalfe KA, Tan HJ, Mohanraj R, Avula S, Williams D, Brady LI, Mesterman R, Tarnopolsky MA, Zhang Y, Yang Y, Wang X, Genomics England Research Consortium, Rees MI, Goldfarb M, Chung SK. Am J Hum Genet 108: 2021 176-185	13
The contribution of X-linked coding variation to severe developmental disorders. Martin HC, Gardner EJ, Samocha KE, Kaplanis J, Akawi N, Sifrim A, Eberhardt RY, Tavares ALT, Neville MDC, Niemi MEK, Gallone G, McRae J, Deciphering Developmental Disorders Study, Wright CF, FitzPatrick DR, Firth HV, Hurles ME. Nat Commun 12: 2021 627	25
Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms. Wright CF, Quaife NM, Ramos-Hernández L, Danecek P, Ferla MP, Samocha KE, Kaplanis J, Gardner EJ, Eberhardt RY, Chao KR, Karczewski KJ, Morales J, Gallone G, Balasubramanian M, Banka S, Gompertz L, Kerr B, Kirby A, Lynch SA, Morton JEV, Pinz H, Sansbury FH, Stewart H, Zuccarelli BD, Genomics England Research Consortium, Cook SA, Taylor JC, Juusola J, Retterer K, Firth HV, Hurles ME, Lara-Pezzi E, Barton PJR, Whiffin N. Am J Hum Genet 108: 2021 1083-1094	34
Detecting cryptic clinically relevant structural variation in exome-sequencing data increases diagnostic yield for developmental disorders. Gardner EJ, Sifrim A, Lindsay SJ, Prigmore E, Rajan D, Danecek P, Gallone G, Eberhardt RY, Martin HC, Wright CF, FitzPatrick DR, Firth HV, Hurles ME. Am J Hum Genet 108: 2021 2186-2194	11
Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases. Yuan X, Wang J, Dai B, Sun Y, Zhang K, Chen F, Peng Q, Huang Y, Zhang X, Chen J, Xu X, Chuan J, Mu W, Li H, Fang P, Gong Q, Zhang P. Brief Bioinform 23: 2022 bbac019	20
Genetic and chemotherapeutic influences on germline hypermutation. Kaplanis J, Ide B, Sanghvi R, Neville M, Danecek P, Coorens T, Prigmore E, Short P, Gallone G, McRae J, Genomics England Research Consortium, Carmichael J, Barnicoat A, Firth H, O'Brien P, Rahbari R, Hurles M. Nature 605: 2022 503-508	45
X-CAP improves pathogenicity prediction of stopgain variants. Rastogi R, Stenson PD, Cooper DN, Bejerano G. Genome Med 14: 2022 81	2
Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders. Wang T, Kim CN, Bakken TE, Gillentine MA, Henning B, Mao Y, Gilissen C, SPARK Consortium, Nowakowski TJ, Eichler EE. Proc Natl Acad Sci U S A 119: 2022 e2203491119	29
IMPROVE-DD: Integrating multiple phenotype resources optimizes variant evaluation in genetically determined developmental disorders. Aitken S, Firth HV, Wright CF, Hurles ME, FitzPatrick DR, Semple CA. HGG Adv 4: 2023 100162	2
Hypothesis-free phenotype prediction within a genetics-first framework. Lu C, Zaucha J, Gam R, Fang H, Ben Smithers, Oates ME, Bernabe-Rubio M, Williams J, Zelenka N, Pandurangan AP, Tandon H, Shihab H, Kalaivani R, Sung M, Sardar AJ, Tzovoras BG, Danovi D, Gough J. Nat Commun 14: 2023 919	2
Evaluation of in silico pathogenicity prediction tools for the classification of small in-frame indels. Cannon S, Williams M, Gunning AC, Wright CF. BMC Med Genomics 16: 2023 36	3
Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland. Wright CF, Campbell P, Eberhardt RY, Aitken S, Perrett D, Brent S, Danecek P, Gardner EJ, Chundru VK, Lindsay SJ, Andrews K, Hampstead J, Kaplanis J, Samocha KE, Middleton A, Foreman J, Hobson RJ, Parker MJ, Martin HC, FitzPatrick DR, Hurles ME, Firth HV, DDD Study. N Engl J Med 388: 2023 1559-1571	56
Sex difference contributes to phenotypic diversity in individuals with neurodevelopmental disorders. Cuppens T, Shatto J, Mangnier L, Kumar AA, Ng AC, Kaur M, Bui TA, Leclercq M, Droit A, Dunham I, Bolduc FV. Front Pediatr 11: 2023 1172154	0
Developing a cluster-based approach for deciphering complexity in individuals with neurodevelopmental differences. Cuppens T, Kaur M, Kumar AA, Shatto J, Ng AC, Leclercq M, Reformat MZ, Droit A, Dunham I, Bolduc FV. Front Pediatr 11: 2023 1171920	0
Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases. Yuan X, Su J, Wang J, Dai B, Sun Y, Zhang K, Li Y, Chuan J, Tang C, Yu Y, Gong Q. Sci Rep 14: 2024 2845	0
Investigating the role of common cis-regulatory variants in modifying penetrance of putatively damaging, inherited variants in severe neurodevelopmental disorders. Wigdor EM, Samocha KE, Eberhardt RY, Chundru VK, Firth HV, Wright CF, Hurles ME, Martin HC. Sci Rep 14: 2024 8708	2
Complex trait associations in rare diseases and impacts on Mendelian variant interpretation. Smail C, Ge B, Keever-Keigher MR, Schwendinger-Schreck C, Cheung WA, Johnston JJ, Barrett C, Genomic Answers for Kids Consortium, Feldman K, Cohen ASA, Farrow EG, Thiffault I, Grundberg E, Pastinen T. Nat Commun 15: 2024 8196	1
Federated analysis of autosomal recessive coding variants in 29,745 developmental disorder patients from diverse populations. Chundru VK, Zhang Z, Walter K, Lindsay SJ, Danecek P, Eberhardt RY, Gardner EJ, Malawsky DS, Wigdor EM, Torene R, Retterer K, Wright CF, Ólafsdóttir H, Guillen Sacoto MJ, Ayaz A, Akbeyaz IH, Türkdoğan D, Al Balushi AI, Bertoli-Avella A, Bauer P, Szenker-Ravi E, Reversade B, McWalter K, Sheridan E, Firth HV, Hurles ME, Samocha KE, Ustach VD, Martin HC. Nat Genet 56: 2024 2046-2053	2
Examining the role of common variants in rare neurodevelopmental conditions. Huang QQ, Wigdor EM, Malawsky DS, Campbell P, Samocha KE, Chundru VK, Danecek P, Lindsay S, Marchant T, Koko M, Amanat S, Bonfanti D, Sheridan E, Radford EJ, Barrett JC, Wright CF, Firth HV, Warrier V, Strudwick Young A, Hurles ME, Martin HC. Nature 636: 2024 404-411	0
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