Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs.

Hb S/b + -thalassemia due to Hb sickle and a novel deletion of DNase I hypersensitive sites HS3 and HS4 of the b locus control region Sickle cell disease (SCD) is one of the most common genetic disorders worldwide and is associated with episodes of acute pain and progressive multi-organ damage. 1 The most common cause of SCD is homozygosity for the hemoglobin sickle (Hb S) mutation, with a minority of cases due to compound heterozygosity for Hb S and other alleles including b-thalassemia. Loss-of-function point mutations of the b-globin gene that abolish (b 0 ) or reduce (b + ) production of normal b-chains are the most common causes of b-thalassemia, with large deletions or rearrangements accounting for a small minority of b-thalassemia alleles.2,3 While patients with Hb S/b 0 -thalassemia generally have severe SCD, the residual production of normal b-chains in Hb S/b + -thalassemia patients is associated with lower Hb S concentration in erythrocytes and a less severe disease. 4 Here, we report the unusual case of an infant who had a newborn screening profile fully consistent with sickle trait, yet was diagnosed later in childhood with typical Hb S/b + -thalassemia. Molecular testing demonstrated that the child was a compound heterozygote for the Hb S mutation and a partial deletion of the b-globin Locus Control Region (bLCR). The deletion removed two of the five DNase I hypersensitivity (HS) regions, providing valuable insight into the roles of individual HS regions in globin gene switching and expression. The proband is now a 6-year old boy who was born to healthy non-consanguineous parents of Caribbean descent. The pregnancy and delivery were unremarkable with no evidence of perinatal anemia or jaundice. Newborn screening was negative for SCD, with the Hb profile being fully consistent with sickle trait (Hb F 79.1%, Hb A 6.0%, Hb S 4.0%, Hb Bart's 9.1%) ( Figure 1A). The patient enjoyed normal health until five years of age, when he was diagnosed with SCD during an admission for unexplained abdominal pain and enlarged spleen (splenic sequestration). Microcytosis, sickle erythrocytes, Howell-Jolly bodies and target cells were observed on the peripheral blood smear. Hemoglobin analysis using high performance liquid chromatography (HPLC) was suggestive of Hb S/b + -thalassemia (Hb A 19.4%, Hb S 72.7%, and Hb A2 2.6%) ( Figure 1B). Since diagnosis, the patient has been admitted for one vasoocclusive event and had a tonsillectomy for obstructive sleep apnea. Nucleotide sequence analysis of the β-gobin gene revealed that the proband was heterozygous for the Hb S mutation (HBB:c.20A>T) with no other mutations of the b-globin gene. Deletion-specific gap-PCR demonstrated that he was also heterozygous for the rightward 3.7 kb single a-globin gene deletion (−a 3.7 /aa). Sequence analysis of the intact aglobin genes failed to detect any point mutations. As this genotype could not explain the reduced expression of Hb A and the SCD phenotype in the proband, we investigated the possibility of compound heterozygosity f...

We report two novel β-thalassemia (β-thal) deletions involving the 5' region of the β-globin gene (HBB). The first deletion spans 538 bp and removes the β-globin promoter, 5' untranslated region (5'UTR) and most of exon 1. This deletion was identified in a 3-year-old Vietnamese boy with non transfusion dependent Hb E (HBB: c.79G>A)/β-thal. The second deletion spans 1517 bp and removes the β-globin gene promoter, 5'UTR, and exons 1 and 2. This deletion was identified in two unrelated adults of European descent who had β-thal trait with unusually high Hb A levels. Deletions such as these are generally associated with higher levels of Hb A and Hb F than typical β-thal alleles, which may ameliorate the severity of the disease.