Target enrichment and high-throughput sequencing of 80 ribosomal protein genes to identify mutations associated with Diamond-Blackfan anaemia

British Journal of Haematology

Volumn 162, Issue 4, 2013, Pages 530-536

  Gerrard, Gareth ^a   Valgañón, Mikel ^a   Foong, Hui En ^a   Kasperaviciute, Dalia ^b   Iskander, Deena ^a   Game, Laurence ^b   Müller, Michael ^b   Aitman, Timothy J ^b   Roberts, Irene ^a,c   de la Fuente, Josu ^a,c   Foroni, Letizia ^a   Karadimitris, Anastasios ^a  

^a HAMMERSMITH HOSPITAL   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c IMPERIAL COLLEGE HEALTHCARE NHS TRUST   (United Kingdom)

Author keywords

Diamond Blackfan anaemia; Molecular diagnostics; Next generation sequencing; Target enrichment

Indexed keywords

RIBOSOME PROTEIN;

ADOLESCENT; ADULT; ARTICLE; BLACKFAN DIAMOND ANEMIA; BLOOD TRANSFUSION; CHILD; CLINICAL ARTICLE; CONTROLLED STUDY; FEMALE; FRAMESHIFT MUTATION; GENE DELETION; GENE INSERTION; GENE MUTATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC SCREENING; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; MALE; NONSENSE MUTATION; PRESCHOOL CHILD; PRIORITY JOURNAL; RIBOSOMAL PROTEIN GENE; SCHOOL CHILD; SINGLE NUCLEOTIDE POLYMORPHISM; TARGET ENRICHMENT;

DIAMOND-BLACKFAN ANAEMIA; MOLECULAR DIAGNOSTICS; NEXT GENERATION SEQUENCING; TARGET ENRICHMENT;

ADOLESCENT; ADULT; ANEMIA, DIAMOND-BLACKFAN; CHILD; CHILD, PRESCHOOL; CODON, NONSENSE; DNA MUTATIONAL ANALYSIS; DNA, RIBOSOMAL; FEMALE; FRAMESHIFT MUTATION; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; RIBOSOMAL PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION;

EID: 84880653370     PISSN: 00071048     EISSN: 13652141     Source Type: Journal    
DOI: 10.1111/bjh.12397     Document Type: Article

References (15)

1. Doherty, L., Sheen, M.R., Vlachos, A., Choesmel, V., O'Donohue, M.F., Clinton, C., Schneider, H.E., Sieff, C.A., Newburger, P.E., Ball, S.E., Niewiadomska, E., Matysiak, M., Glader, B., Arceci, R.J., Farrar, J.E., Atsidaftos, E., Lipton, J.M., Gleizes, P.E. & Gazda, H.T. (2010) Ribosomal protein genes RPS10 and RPS26 are commonly mutated in Diamond-Blackfan anemia. American Journal of Human Genetics, 86, 222-228.
2. Draptchinskaia, N., Gustavsson, P., Andersson, B., Pettersson, M., Willig, T.N., Dianzani, I., Ball, S., Tchernia, G., Klar, J., Matsson, H., Tentler, D., Mohandas, N., Carlsson, B. & Dahl, N. (1999) The gene encoding ribosomal protein S19 is mutated in Diamond-Blackfan anaemia. Nature Genetics, 21, 169-175.
3. Farrar, J.E. & Dahl, N. (2011) Untangling the phenotypic heterogeneity of Diamond Blackfan anemia. Seminars in Hematology, 48, 124-135.
4. Farrar, J.E., Vlachos, A., Atsidaftos, E., Carlson-Donohoe, H., Markello, T.C., Arceci, R.J., Ellis, S.R., Lipton, J.M. & Bodine, D.M. (2011) Ribosomal protein gene deletions in Diamond-Blackfan anemia. Blood, 118, 6943-6951.
5. Gazda, H.T., Zhong, R., Long, L., Niewiadomska, E., Lipton, J.M., Ploszynska, A., Zaucha, J.M., Vlachos, A., Atsidaftos, E., Viskochil, D.H., Niemeyer, C.M., Meerpohl, J.J., Rokicka-Milewska, R., Pospisilova, D., Wiktor-Jedrzejczak, W., Nathan, D.G., Beggs, A.H. & Sieff, C.A. (2004) RNA and protein evidence for haplo-insufficiency in Diamond-Blackfan anaemia patients with RPS19 mutations. British Journal of Haematology, 127, 105-113.
6. Gazda, H.T., Preti, M., Sheen, M.R., O'Donohue, M.F., Vlachos, A., Davies, S.M., Kattamis, A., Doherty, L., Landowski, M., Buros, C., Ghazvinian, R., Sieff, C.A., Newburger, P.E., Niewiadomska, E., Matysiak, M., Glader, B., Atsidaftos, E., Lipton, J.M., Gleizes, P.E. & Beggs, A.H. (2012) Frameshift mutation in p53 regulator RPL26 is associated with multiple physical abnormalities and a specific pre-ribosomal RNA processing defect in diamond-blackfan anemia. Human Mutation, 33, 1037-1044.
7. Ito, E., Yoshida, Y., Yusuke Okuno, Y., Sato-Otsubo, A., Toki, T., Miyano, S., Shiraishi, Y., Chiba, K., Terui, K., Wang, R., Sato, T., Iribe, Y., Ohga, S., Kuramitsu, M., Hamaguchi, I., Ohara, A., Kudo, K., Kamimaki, I., Hara, J., Sugita, K., Matsubara, K., Koike, K., Ishiguro, A., Kawano, Y., Kanno, H., Kojima, S. & Ogawa, S. (2012) Identification of Two New DBA Genes, RPS27 and RPL27, by Whole-Exome Sequencing in Diamond-Blackfan Anemia Patients. Blood (ASH Annual Meeting Abstracts), 120, 984.
8. Konno, Y., Toki, T., Tandai, S., Xu, G., Wang, R., Terui, K., Ohga, S., Hara, T., Hama, A., Kojima, S., Hasegawa, D., Kosaka, Y., Yanagisawa, R., Koike, K., Kanai, R., Imai, T., Hongo, T., Park, M.J., Sugita, K. & Ito, E. (2010) Mutations in the ribosomal protein genes in Japanese patients with Diamond-Blackfan anemia. Haematologica, 95, 1293-1299.
9. Li, H. & Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
10. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. & Durbin, R. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England), 25, 2078-2079.
11. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M. & DePristo, M.A. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297-1303.
12. Mirabello, L., Ballew, B., Giri, N., Jacobs, K., Yeager, M., Boland, J., Hicks, B., Burdett, L., Hutchinson, A., Alter, B. & Savage, S. (2012) RPS29 is mutated in a multi-case diamond blackfan anemia family. Blood (ASH Annual Meeting Abstracts), 120, 511.
13. Sankaran, V.G., Ghazvinian, R., Do, R., Thiru, P., Vergilio, J.A., Beggs, A.H., Sieff, C.A., Orkin, S.H., Nathan, D.G., Lander, E.S. & Gazda, H.T. (2012) Exome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia. The Journal of Clinical Investigation, 122, 2439-2443.
14. Vlachos, A., Ball, S., Dahl, N., Alter, B.P., Sheth, S., Ramenghi, U., Meerpohl, J., Karlsson, S., Liu, J.M., Leblanc, T., Paley, C., Kang, E.M., Leder, E.J., Atsidaftos, E., Shimamura, A., Bessler, M., Glader, B. & Lipton, J.M. (2008) Diagnosing and treating Diamond Blackfan anaemia: results of an international clinical consensus conference. British Journal of Haematology, 142, 859-876.
15. Wang, K., Li, M. & Hakonarson, H. (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38, e164.