Whole-genome sequencing for optimized patient management

Abstract

Whole-genome sequencing of patient DNA can facilitate diagnosis of a disease, but its potential for guiding treatment has been under-realized. We interrogated the complete genome sequences of a 14-year-old fraternal twin pair diagnosed with dopa (3,4-dihydroxyphenylalanine)-responsive dystonia (DRD; Mendelian Inheritance in Man #128230). DRD is a genetically heterogeneous and clinically complex movement disorder that is usually treated with l-dopa, a precursor of the neurotransmitter dopamine. Whole-genome sequencing identified compound heterozygous mutations in the SPR gene encoding sepiapterin reductase. Disruption of SPR causes a decrease in tetrahydrobiopterin, a cofactor required for the hydroxylase enzymes that synthesize the neurotransmitters dopamine and serotonin. Supplementation of l-dopa therapy with 5-hydroxytryptophan, a serotonin precursor, resulted in clinical improvements in both twins.

Fig. 1

Metabolic pathways of neurotransmitter production. DRD has been associated with mutations in the genes encoding GTP cyclohydrolase (GCH1), tyrosine hydroxylase (TH), and sepiapterin reductase (SPR) (boxed), which are enzymes associated with production of the neurotransmitters dopamine and serotonin. The catalytic action of GCH1 is the rate-limiting step in production of tetrahydrobiopterin (BH4), a cofactor for the tyrosine and tryptophan hydroxylases. Disruption of the GCH1 gene can cause autosomal dominant DRD. Autosomal recessive DRD is caused by mutations in TH and SPR. Both 5-hydroxytryptophan (5-HTP) and dopamine production are disrupted by mutations in SPR whereas only dopamine production is disrupted by mutations in TH.

Fig. 2

Pedigree of a family segregating recessive DRD, depression, and fibromyalgia. Pedigree of the family with the two DRD-affected probands (shaded), male and female fraternal twins. Their DRD is due to disruption of SPR activity resulting in impaired BH4 cofactor synthesis, leading to disruption in the production of the neurotransmitters dopamine, noradrenaline, and serotonin. In addition to DRD in the probands, the family has a history of depression and fibromyalgia on either side of the pedigree. Segregation of the two SPR mutations is shown for all individuals evaluated.

Fig. 3

Validation and segregation of two deleterious SPR alleles. Shown is the pedigree of the two DRD-affected probands (shaded), their unaffected sibling, and their parents. Squares indicate male subjects and circles female subjects. The Sanger sequencing traces showing the SPR genotype of each member of the pedigree are shown. p.Arg150Gly refers to the A→G mutation on chromosome 2 at nucleotide 72,969,094, leading to the amino acid missense mutation; p.Lys251X indicates the A→T mutation on chromosome 2 at nucleotide 72,972,139, causing an amino acid nonsense mutation. The variants are deleterious to SPR activity but have only been observed, separately, as homozygous mutations from presumed consanguineous kindreds. The unaffected mother is homozygous (A/A) for the wild-type allele at the first locus but heterozygous (A/T) for the pathogenic p.Lys251X allele at the second locus. Similarly, the unaffected father is heterozygous (A/G) for the pathogenic p.Arg150Gly allele at the first locus and homozygous (A/A) for the wild-type allele at the second locus. Each DRD-affected proband is heterozygous (A/G and A/T) for the pathogenic mutations at both alleles, indicating a new compound heterozygous combination of mutant alleles that is causative for DRD. The mutations result in reduction of SPR-mediated synthesis of BH4, a coenzyme needed for neurotransmitter production. Absence or reduction of the neurotransmitter dopamine causes distinct clinical symptoms including dystonia.