SUPPLEMENTARY MATERIAL
Infantile Leigh-like syndrome caused by SLC19A3 mutations is a
treatable disease
Tobias B. Haack1, 2, Dirk Klee3, Tim M. Strom1, 2, Thomas Meitinger1, 2, Ertan Mayatepek4,
Holger Prokisch1, 2#, Felix Distelmaier4#
1
Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
2
3
4
Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
Department of Diagnostic and Interventional Radiology, Heinrich-Heine University, Düsseldorf, Germany
Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, HeinrichHeine University, Düsseldorf, Germany
SUPPLEMENTARY METHODS
Exome sequencing and variant filtering
We used exome sequencing to investigate the genetic basis of the disease in patient #74115. Genomic
DNA was extracted from patient-derived fibroblast cell lines using standard protocols. A SureSelect
Human All Exon 50 Mb V5 Kit (Agilent) was used for enrichment of coding DNA fragments. Sequencing
was performed on a HiSeq2000 system (Illumina). BWA (version 0.5.8) was used for read alignment to
the human reference assembly (hg19) and single-nucleotide variants (SNVs) and small insertions and
deletions were detected with SAMtools (version 0.1.7). For detailed sequencing statistics see
Supplementary Table 1.
Prioritization of candidate disease genes was essentially performed as reported previously (Haack et al.,
2012). The analysis was focused on non-synonymous variants. Based on the rare disease phenotype we
expected the disease-causal mutations to have a low frequency in general populations. We therefore
excluded variants present in 3,600 control exomes and public databases. Furthermore, we assumed an
autosomal recessive mode of inheritance. Accordingly, we searched for genes carrying predicted
compound heterozygous or homozygous mutations. This filter left 28 genes. Only one gene, SLC19A3,
carried two predicted loss-of-function alleles (Supplementary Table 2).
Primers and PCR conditions for confirmatory Sanger sequencing are provided upon request.
References
Haack TB, Haberberger B, Frisch EM, Wieland T, Iuso A, Gorza M, et al. Molecular diagnosis in
mitochondrial complex I deficiency using exome sequencing. Journal of medical genetics. 2012
Apr;49(4):277-83.
SUPPLEMENTARY TABLES
Supplementary Table 1 Next generation sequencing statistics
Id
Type
#74115 SureSelect50Mb V5
Reads
Mapped
105200293 104391066
Percent
Seq (Gb) on bait
Avg
cov
Cov
1x
Cov
4x
Cov
8x
Cov
20x
99.23
10.63
126.73 99.9
99.7
99.3
97.1
76.12
Supplementary Table 2 Variants identified at different filtering levels in individual #74115.
Variants filtering
Synonymous variants
11,628
Non-synonymous variants (NSV)
12,304
NSV absent from 3,600 control exomes and public databases
213
Genes carrying > 2 NSV
28
Genes carrying > 2 loss-of-function alleles
1 (SLC19A3)
NSV = missense, nonsense, stop/loss, splice site disruption, insertions, deletions