Fast clinical molecular diagnosis of hyperphenylalaninemia using next-generation sequencing-based on a custom AmpliSeq™ panel and Ion Torrent PGM sequencing

Molecular Genetics and Metabolism

Volumn 113, Issue 4, 2014, Pages 261-266

  Cao, Yan Yan ^a   Qu, Yu Jin ^a   Song, Fang ^a   Zhang, Ting ^a   Bai, Jin Li ^a   Jin, Yu Wei ^a   Wang, Hong ^a  

^a CAPITAL INSTITUTE OF PEDIATRICS   (China)

Author keywords

Hyperphenylalaninemia; Ion Torrent PGM sequencing; Metabolic pathway; Molecular diagnosis

Indexed keywords

6 PYRUVOYLTETRAHYDROPTERIN SYNTHASE; ARGININE; ASPARAGINE; DIHYDROPTERIDINE REDUCTASE; GLUTAMIC ACID; GLUTAMINE; GUANOSINE TRIPHOSPHATE CYCLOHYDROLASE I; ISOLEUCINE; LEUCINE; METHIONINE; PHENYLALANINE; PHENYLALANINE 4 MONOOXYGENASE; PROLINE; PROTEIN; PTERIN 4 ALPHA CARBINOLAMINE DEHYDRATASE; SERINE; THREONINE; TYROSINE; UNCLASSIFIED DRUG; VALINE; HYDROLYASE; PTERIN-4A-CARBINOLAMINE DEHYDRATASE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ALLELE; AMPLICON; ARTICLE; DIFFERENTIAL DIAGNOSIS; DNA FLANKING REGION; DNA SEQUENCE; FRAMESHIFT MUTATION; GENE DELETION; GENE FREQUENCY; GENE MUTATION; GENETIC ANALYZER; HETEROZYGOTE; HIGH THROUGHPUT SEQUENCING; HOMOZYGOTE; HUMAN; HYPERPHENYLALANINEMIA; INDEL MUTATION; INTRON; ION TORRENT PERSONAL GENOME MACHINE; ION TORRENT PERSONAL GENOME MACHINE SEQUENCING; MAJOR CLINICAL STUDY; MISSENSE MUTATION; MOLECULAR DIAGNOSIS; NONSENSE MUTATION; SANGER SEQUENCING; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; CASE REPORT; GENETICS; MUTATION; NEWBORN; NEWBORN SCREENING; NUCLEOTIDE SEQUENCE; PHENYLKETONURIAS; PROCEDURES;

BASE SEQUENCE; FRAMESHIFT MUTATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; HYDRO-LYASES; INFANT, NEWBORN; MUTATION; NEONATAL SCREENING; PHENYLALANINE HYDROXYLASE; PHENYLKETONURIAS; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION;

EID: 84919387166     PISSN: 10967192     EISSN: 10967206     Source Type: Journal    
DOI: 10.1016/j.ymgme.2014.10.004     Document Type: Article

References (15)

1. Werner E.R., Blau N., Thöny B. Tetrahydrobiopterin: biochemistry and pathophysiology. Biochem. J. 2011, 438:397-414.
2. Rothberg J.M., Hinz W., Rearick T.M., Schultz J., Mileski W., Davey M., Leamon J.H., Johnson K., Milgrew M.J., Edwards M., Hoon J., Simons J.F., Marran D., Myers J.W., Davidson J.F., Branting A., Nobile J.R., Puc B.P., Light D., Clark T.A., Huber M., Branciforte J.T., Stoner I.B., Cawley S.E., Lyons M., Fu Y., Homer N., Sedova M., Miao X., Reed B., Sabina J., Feierstein E., Schorn M., Alanjary M., Dimalanta E., Dressman D., Kasinskas R., Sokolsky T., Fidanza J.A., Namsaraev E., McKernan K.J., Williams A., Roth G.T., Bustillo J. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475:348-352.
3. Abou Tayoun A.N., Tunkey C.D., Pugh T.J., Ross T., Shah M., Lee C.C., Harkins T.T., Wells W.A., Tafe L.J., Amos C.I., Tsongalis G.J. A comprehensive assay for CFTR mutational analysis using nest-generation sequencing. Clin. Chem. 2013, 59:1481-1488.
4. Costa J.L., Sousa S., Justino A., Kay T., Fernandes S., Cirnes L., Schmitt F., Machado J.C. Nonoptical massive parallel DNA sequencing of BRCA1 and BRCA2 genes in a diagnostic setting. Hum. Mutat. 2013, 34:629-635.
5. Li X., Buckton A.J., Wilkinson S.L., John S., Walsh R., Novotny T., Valaskova I., Gupta M., Game L., Barton P.J., Cook S.A., Ware J.S. Towards clinical molecular diagnosis of inherited cardiac conditions: a comparison of bench-top genome DNA sequencers. PLoS One 2013, 8:e67744.
6. Millat G., Chanavat V., Rousson R. Evaluation of a new high-throughput next-generation sequencing method based on a custom Ampliseq™ library and Ion Torrent PGM™ sequencing for the rapid detection of genetic variations in long QT syndrome. Mol. Diagn. Ther. 2014, 18:533-539.
7. Millat G., Chanavat V., Rousson R. Evaluation of a new NGS method based on a custom AmpliSeq library and Ion Torrent PGM sequencing for the fast detection of genetic variations in cardiomyopathies. Clin. Chim. Acta 2014, 433:266-271.
8. Song F., Qu Y.J., Zhang T., Jin Y.W., Wang H., Zheng X.Y. Phenylketonuria mutations in Northern China. Mol. Genet. Metab. 2005, 86:S107-S118.
9. Schwarz J.M., Cooper D.N., Schuelke M., Seelow D. MutationTaster2: mutation prediction for the deep-sequencing age. Nat. Methods 2014, 11:361-362.
10. Cao Y., Yuan P., Wang Y.P., Mao M., Zhu J. The profile of newborn screening coverage in China. J. Med. Screen. 2009, 16:163-166.
11. Bashyam M.D., Chaudhary A.K., Reddy E.C., Devi A.R., Savithri G.R., Ratheesh R., Bashyam L., Mahesh E., Sen D., Puri R., Verma I.C., Nampoothiri S., Vaidyanathan S., Chandrashekar M.D., Kantheti P. Phenylalanine hydroxylase gene mutations in phenylketonuria patients from India: identification of novel mutations that affect PAH RNA. Mol. Genet. Metab. 2010, 100:96-99.
12. Kozak L., Hrabincova E., Kintr J., Horky O., Zapletalova P., Blahakova I., Mejstrik P., Prochazkova D. Identification and characterization of large deletions in the phenylalanine hydroxylase (PAH) gene by MLPA: evidence for both homologous and non-homologous mechanisms of rearrangement. Mol. Genet. Metab. 2006, 89:300-309.
13. Chan M., Ji S.M., Yeo Z.X., Gan L., Yap E., Yap Y.S., Ng R., Tan P.H., Ho G.H., Ang P., Lee A.S. Development of a next-generation sequencing method for BRCA mutation screening. J. Mol. Diagn. 2012, 14:602-612.
14. Trujillano D., Perez B., González J., Tornador C., Navarrete R., Escaramis G., Ossowski S., Armengol L., Cornejo V., Desviat L.R., Ugarte M., Estivill X. Accurate molecular diagnosis of phenylketonuria and tetrahydrobiopterin-deficient hyperphenylalaninemias using high-throughput targeted sequencing. Eur. J. Hum. Genet. 2014, 22:528-534.
15. Gu Y., Lu K., Yang G., Cen Z., Yu L., Lin L., Hao J., Yang Z., Peng J., Cui S., Huang J. Mutation spectrum of six genes in Chinese phenylketonuria patients obtained through next-generation sequencing. PLoS One 2014, 9:e94100.