Spinal muscular atrophies (SMAs) are a heterogeneous group of
neuromuscular diseases characterized by loss of motor neurons, muscle
weakness, hypotonia and muscle atrophy, with different modes of
inheritance; however, the survival motor neuron 1 (SMN1) gene is
predominantly involved. The aims of the current study were to clarify
the genetic basis of SMA and determine the mutation spectrum of SMN1 and
other associated genes, in order to provide molecular information for
more accurate diagnosis and future prospects for treatment. We performed
a comprehensive analysis of 5q SMA in 1765 individuals including 528
patients from 432 unrelated families with at least one child with
suspected clinical presentation of SMA. Copy number variations of the
SMN1 and SMN2 genes and linkage analysis were performed using multiplex
ligation-dependent probe amplification (MLPA) and short tandem repeat
(STR) markers linked to the SMN1 gene. Cases without mutation in the SMA
locus on 5q were analyzed for the DNAJB2, IGHMBP2, SIGMAR1 and PLEKHG5
genes using linked STR markers. Sanger sequencing of whole genes was
performed for cases with homozygous haplotypes. Whole-genome sequencing
(WGS) and whole-exome analysis was conducted for some of the remaining
cases. Mutations in the SMN1 gene were identified in 287 (66.43%)
families including 269 patients (62.26%) with homozygous deletion of the
entire SMN1 gene. Only one of the patients had a homozygous point
mutation in the SMN1 gene. Among the remaining families, three families
showed mutations in either the DNAJB2, SIGMAR1 or PLEKHG5 genes, which
were linked using STR analysis and Sanger sequencing. From 10 families
who underwent WGS, we found six homozygous point mutations in six
families for either the TNNT1, TPM3, TTN, SACS or COL6A2 genes. Two
mutations in the PLA2G6 gene were also found in another patient as
compound heterozygous. This rather large cohort allowed us to identify
genotype patterns in Iranian 5q SMA patients. The process of identifying
11 mutations (9 novel) in 9 different genes among non-5q SMA patients
shows the diversity of genes involved in non-5q SMA in Iranians.
Genotyping of patients with SMA is essential for prenatal and
preimplantation genetic diagnosis (PGD), and may be very helpful for
guiding treatment, with the advent of new, more effective, albeit very
expensive, therapies. Also, combining linkage analysis was shown to be
beneficial in many ways, including sample authenticity and segregation
analysis, and for ruling out maternal cell contamination during prenatal
diagnosis (PND).