A high-throughput resequencing microarray for autosomal dominant spastic paraplegia genes.

Claudia Dufke, Nina Schlipf, Rebecca Schüle, Michael Bonin, Michaela Auer-Grumbach, Giovanni Stevanin, Christel Depienne, Jan Kassubek, Stephan Klebe, Sven Klimpe, Thomas Klopstock, Susanne Otto, Sven Poths, Andrea Seibel, Henning Stolze, Andreas Gal, Ludger Schöls, Peter Bauer
Neurogenetics. 2012-05-03; 13(3): 215-227
DOI: 10.1007/s10048-012-0329-6

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1. Neurogenetics. 2012 Aug;13(3):215-27. doi: 10.1007/s10048-012-0329-6. Epub 2012
May 3.

A high-throughput resequencing microarray for autosomal dominant spastic
paraplegia genes.

Dufke C(1), Schlipf N, Schüle R, Bonin M, Auer-Grumbach M, Stevanin G, Depienne
C, Kassubek J, Klebe S, Klimpe S, Klopstock T, Otto S, Poths S, Seibel A, Stolze
H, Gal A, Schöls L, Bauer P.

Author information:
(1)Department of Medical Genetics, Eberhard-Karls-University, Tübingen, Germany.

Hereditary spastic paraplegias (HSP) are a heterogeneous group of neurological
disorders. Insidiously progressive spastic weakness of the lower extremities is
the common criterion in all forms described. Clinically, HSP is differentiated
into pure (uncomplicated) and complex (complicated) forms. While pure HSP is
predominantly characterized by signs and symptoms of pyramidal tract dysfunction,
additional neurological and non-neurological symptoms occur in complicated forms.
Autosomal dominant, autosomal recessive, and X-linked modes of inheritance have
been described and at least 48 subtypes, termed SPG1-48, have been genetically
defined. Although in autosomal dominant HSP families 50-60% of etiologies can be
established by genetic testing, genotype predictions based on the phenotype are
limited. In order to realize high-throughput genotyping for dominant HSP, we
designed a resequencing microarray for six autosomal dominant genes on the
Affymetrix CustomSEQ array platform. For validation purposes, 10 previously
Sanger sequenced patients with autosomal dominant HSP and 40 positive controls
with known mutations in ATL1, SPAST, NIPA1, KIF5A, and BSCL2 (32 base exchanges,
eight small indels) were resequenced on this array. DNA samples of 45 additional
patients with AD spastic paraplegia were included in the study. With two
different sequencing analysis software modules (GSEQ, SeqC), all
missense/nonsense mutations in the positive controls were identified while indels
had a detection rate of only 50%. In total, 244 common synonymous
single-nucleotide polymorphisms (SNPs) annotated in dbSNP (build 132)
corresponding to 22 distinct sequence variations were found in the 53 analyzed
patients. Among the 22 different sequence variations (SPAST n = 15, ATL1 n = 3,
KIF5A n = 2, HSPD1 n = 1, BSCL2 n = 1, NIPA1 n = 0), 12 were rare variants that
have not been previously described and whose clinical significance is unknown. In
SPAST-negative cases, a genetic diagnosis could be established in 11% by
resequencing. Resequencing microarray technology can therefore efficiently be
used to study genotypes and mutations in large patient cohorts.

DOI: 10.1007/s10048-012-0329-6
PMID: 22552817 [Indexed for MEDLINE]

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