Diagnosis and discovery: Insights from the NIH Undiagnosed Diseases Program

Abstract

Living with an undiagnosed medical condition places a tremendous burden on patients, their families, and their healthcare providers. The Undiagnosed Diseases Program (UDP) was established at the National Institutes of Health (NIH) in 2008 with the primary goals of providing a diagnosis for patients with mysterious conditions and advancing medical knowledge about rare and common diseases. The program reviews applications from referring clinicians for cases that are considered undiagnosed despite a thorough evaluation. Those that are accepted receive clinical evaluations involving deep phenotyping and genetic testing that includes exome and genomic sequencing. Selected candidate gene variants are evaluated by collaborators using functional assays. Since its inception, the UDP has received more than 4500 applications and has completed evaluations on nearly 1300 individuals. Here we present six cases that exemplify the discovery of novel disease mechanisms, the importance of deep phenotyping for rare diseases, and how genetic diagnoses have led to appropriate treatment. The creation of the Undiagnosed Diseases Network (UDN) in 2014 has substantially increased the number of patients evaluated and allowed for greater opportunities for data sharing. Expansion to the Undiagnosed Diseases Network International (UDNI) has the possibility to extend this reach even farther. Together, networks of undiagnosed diseases programs are powerful tools to advance our knowledge of pathophysiology, accelerate accurate diagnoses, and improve patient care for patients with rare conditions.

Keywords: CHST14; CLCN7; KMT2B; NT5E; SNORD118; SNP microarray; Undiagnosed Diseases Program; amyloidosis; exome sequencing; whole genome sequencing.

FIGURE 1

Clinical, biochemical, and histologic findings in patients with NT5E-associated calcification of the joints and arteries (A) Plain radiographs from the proband demonstrating calcification. Upper left: femoral and popliteal arteries. Upper right: iliac and femoral arteries. Lower: metacarpal phalangeal and interphalangeal joints. (B) Upper: NT5E messenger RNA in patients as compared with controls. Lower: deficiency in CD73 enzyme activity represented by AMP-dependent inorganic phosphate production in cultured fibroblasts from affected patients. (C) The results of staining for tissue-nonspecific alkaline phosphatase (TNAP) in fibroblasts from control and patient after incubation for 3 days in calcifying medium. The increased staining in the patient’s cells (middle image) was reduced by adding 30 μM adenosine to the incubation medium daily (right image).

FIGURE 2

Clinical and histological features of probands with de novo CLCN7 variants. (A) Proband 1 with hypopigmented skin and hair and brown irides. (B) Brain MRI at 20 months displaying delayed myelination. (C, D) Transmission electron micrographs showing abnormal cytoplasmic inclusions in histiocytes of the duodenum (C) and in liver macrophages (D). (E) Blood smear shows vacuoles in a polymorphonuclear leukocyte (PMN). (F) Dermal fibroblasts exhibit enlarged vacuoles. (G) Chloride transport studies showing that fibroblast lysosomal pH is lower in probands than in controls. (H) Heterozygous knock-in F1 mice with Tyr713Cys variant had pigmentation defects compared to wild-type B6J mouse. p.Tyr713Cys in mice corresponds to p.Tyr715Cys in humans. (I) Intensity of LysoTracker^™ Deep Red staining of dermal fibroblasts from probands decreased when treated with chloroquine in a dose-dependent manner. (J) Chloroquine treatment at increasing doses alkalinizes lysosomal pH.

FIGURE 3

Clinical and molecular features of patient with CHST14 mutations. (A) Talipes deformity and slender toes with acrogeria-like fine sole creases. (B, C) Large subcutaneous hematomas in upper (B) and lower extremities with evidence of hemarthrosis (C). (D) Tapered fingers with contractures of distal interphalangeal joints. (E) Sanger sequencing confirmed a homozygous missense variant in the single exon of CHST14.

FIGURE 4

Clinical photographs, imaging findings, and histology of the patient with amyloidosis. (A) Photograph of the patient’s back demonstrating paraspinal and trapezius (shoulder pad) muscle enlargement. (B) CT images demonstrating massive enlargement of the paraspinal muscles (upper pane). MR images demonstrating significant bilateral enlargement of all the extraocular muscles (lower pane; arrow indicating the left superior rectus muscle). (C) Cardiac Cine MRI, a technology allowing visualization of blood flow patterns in the heart and great vessels, shows abnormal late gadolinium enhancement of the atrial walls bilaterally (arrows). In the absence of significant cardiac involvement and without cardiac muscle histology, it is uncertain whether this late enhancement in the atria is due to amyloid deposition. (D) Amyloid P immunostaining of paraffin-embedded muscle tissue showed perivascular amyloid deposition. No sarcoplasmic deposits were observed.