Mitzi L. Murray

Genomic and Genic Deletions of the FOX Gene Cluster on 16q24.1 and Inactivating Mutations of FOXF1 Cause Alveolar Capillary Dysplasia and Other Malformations

Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a rare, neonatally lethal developmental disorder of the lung with defining histologic abnormalities typically associated with multiple congenital anomalies (MCA). Using array CGH analysis, we have identified six overlapping microdeletions encompassing the FOX transcription factor gene cluster in chromosome 16q24.1q24.2 in patients with ACD/MPV and MCA. Subsequently, we have identified four different heterozygous mutations (frameshift, nonsense, and no-stop) in the candidate FOXF1 gene in unrelated patients with sporadic ACD/MPV and MCA. Custom-designed, high-resolution microarray analysis of additional ACD/MPV samples revealed one microdeletion harboring FOXF1 and two distinct microdeletions upstream of FOXF1, implicating a position effect. DNA sequence analysis revealed that in six of nine deletions, both breakpoints occurred in the portions of Alu elements showing eight to 43 base pairs of perfect microhomology, suggesting replication error Microhomology-Mediated Break-Induced Replication (MMBIR)/Fork Stalling and Template Switching (FoSTeS) as a mechanism of their formation. In contrast to the association of point mutations in FOXF1 with bowel malrotation, microdeletions of FOXF1 were associated with hypoplastic left heart syndrome and gastrointestinal atresias, probably due to haploinsufficiency for the neighboring FOXC2 and FOXL1 genes. These differences reveal the phenotypic consequences of gene alterations in cis.

Actionable exomic incidental findings in 6503 participants: challenges of variant classification

Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base.

Follow-up of carriers of BRCA1 and BRCA2 variants of unknown significance: Variant reclassification and surgical decisions

Purpose: Approximately 5–10% of patients who undergo genetic testing of BRCA1 and BRCA2 receive a variant of unknown significance (VUS) result. The ambiguous nature of a VUS may increase difficulty in patient understanding and decision making regarding risk reduction and surveillance options, including cancer risk-reducing surgeries. VUS reclassification to benign or deleterious may occur in time; however, clinical decisions may need to be made expeditiously, and some patients may pursue irreversible treatments before VUS reclassification.Methods: We reviewed the surgical decisions of 107 women postdisclosure of a BRCA VUS result counseled at our institute between 1998 and 2009.Conclusion: Among women receiving a BRCA VUS result at our center, 11 of 107 (10.3%) pursued cancer risk-reducing mastectomy and 22 of 107 (20.6%) pursued cancer risk-reducing bilateral salpingo-oophorectomy. Reclassification of VUS occurred up to 9 years after testing, and 5 of 22 (22.7%) women followed up for 8 or more years continue to have a VUS result. We discuss considerations for providers of genetic services to discuss with patients who receive a VUS result.

Pregnancy-related deaths and complications in women with vascular Ehlers-Danlos syndrome

Purpose:The purpose of this study was to characterize the nature and magnitude of pregnancy risks in women with vascular Ehlers–Danlos syndrome.Methods:Pregnancy-related death rate was determined by a review of pedigrees of families with vascular Ehlers–Danlos syndrome. Maternal morbidity was characterized through semistructured interviews with women with vascular Ehlers–Danlos syndrome or their next of kin.Results:Pregnancy-related deaths occurred in 30 of 565 deliveries (5.3%). There was no difference in Kaplan–Meier survival curves between parous versus nulliparous women with vascular Ehlers–Danlos syndrome. Interviews with 39 women indicated that 46% of deliveries were uncomplicated. The most common pregnancy-related complications were third-/fourth-degree lacerations (20%) and preterm delivery (19%). Life-threatening complications occurred in 14.5% of deliveries and included arterial dissection/rupture (9.2%), uterine rupture (2.6%), and surgical complications (2.6%). There were 5 maternal deaths in 76 deliveries (6.5%).Conclusion:The risk of pregnancy-related complications is increased in women with vascular Ehlers–Danlos syndrome compared with the general population; however, survival data indicate that pregnancy does not appear to affect overall mortality compared with nulliparous women with vascular Ehlers–Danlos syndrome. The data were insufficient to determine whether mode or timing of delivery influenced risk of complications. Women with vascular Ehlers–Danlos syndrome should be engaged in a shared decision-making process when contemplating pregnancy and pregnancy management.Genet Med 16 12, 874–880.

Heritable Collagen Disorders: The Paradigm of the Ehlers—Danlos Syndrome

The heritable disorders called Ehlers–Danlos syndrome (EDS) are as disparate as they are fascinating. Their discovery and description has been an intimate part of the growth of our understanding of matrix biology. Joint hypermobility, skin extensibility, abnormal scarring, and tissue friability are the hallmark diagnostic features; however, McKusick (1956) recognized that EDS is under-recognized because when the physical signs are not ‘‘classic’’ the diagnosis may be elusive. The medical and scientific history of EDS can be seen in three phases: clinical characterization, biochemical and molecular genetic analysis, and the use of high throughput genomic analysis to extend the phenotypes.

Ehlers-Danlos syndrome: a showcase of conditions that lead to understanding matrix biology.

The Ehlers-Danlos syndromes (EDS) are genetically and clinically diverse disorders in which affected individuals share a number of physical characteristics, including joint hypermobility, skin extensibility, and tissue friability. Clinical investigations opened the door to identifying the biochemical and molecular etiologies of this diverse but overlapping group of disorders. In this article, we provide an overview of how these disorders inform our understanding of matrix biology, including the role of collagens (types I, III and V), proteoglycans and other proteins.

The challenge of comprehensive and consistent sequence variant interpretation between clinical laboratories

Purpose:Genetic testing has shifted from academic laboratories with expertise in specific genes to commercial laboratories that offer tests of a diverse array of genes. The purpose of this comparative study was to determine whether one academic laboratory’s model of variant interpretation is similar to that of several commercial laboratories.Methods:The Collagen Diagnostic Laboratory (CDL) received, over a 14-month period, 38 requests to interpret variants originally identified by an outside laboratory (OL). The interpretations by the OL and CDL were compared and discrepancies were assessed.Results:Interpretations from the OL and CDL were concordant in 11 inquiries (29%); discrepancies were moderate in 11 instances (29%) and significant in 16 (42%). Factors that caused discrepancies included the following: (i) private data were not shared in a public database (n = 9); (ii) publicly available allele frequency data were not referenced and used as evidence (n = 5); and (iii) important aspects of protein structure and function were not taken into account (n = 13).Conclusion:Comprehensive interpretation of sequence variants depends on good functional tests and well-curated variant databases. Provision of clinical information to the clinical laboratory, mandatory submission of identified variants with phenotype data to common resources, and collaboration between clinical laboratories and recognized experts is likely to improve consistency in variant interpretation among clinical laboratories.Genet Med 18 1, 20–24.

Neuronal migration disorders in microcephalic osteodysplastic primordial dwarfism type I/III.

Microcephalic osteodysplastic primordial dwarfism (MOPD) is a rare microlissencephaly syndrome, with at least two distinct phenotypic and genetic types. MOPD type II is caused by pericentrin mutations, while types I and III appear to represent a distinct entity (MOPD I/III) with variably penetrant phenotypes and unknown genetic basis. The neuropathology of MOPD I/III is little understood, especially in comparison to other forms of lissencephaly. Here, we report postmortem brain findings in an 11-month-old female infant with MOPD I/III. The cerebral cortex was diffusely pachygyric, with a right parietal porencephalic lesion. Histologically, the cortex was abnormally thick and disorganized. Distinct malformations were observed in different cerebral lobes, as characterized using layer-specific neuronal markers. Frontal cortex was severely disorganized and coated with extensive leptomeningeal glioneuronal heterotopia. Temporal cortex had a relatively normal 6-layered pattern, despite cortical thickening. Occipital cortex was variably affected. The corpus callosum was extremely hypoplastic. Brainstem and cerebellar malformations were also present, as well as old necrotic foci. Findings in this case suggest that the cortical malformation in MOPD I/III is distinct from other forms of pachygyria–lissencephaly.

FKBP14-related Ehlers-Danlos syndrome: expansion of the phenotype to include vascular complications.

Biallelic mutations in FKBP14 cause a recessive form of Ehlers‐Danlos syndrome (EDS) characterized by progressive kyphoscoliosis, myopathy, and hearing loss. To date, four children and one adult with this condition have been reported. We recently identified a 42‐year‐old man with severe kyphoscoliosis, restrictive/obstructive lung disease, short stature, mild hearing loss, decreased muscle mass, and a dissection of the celiac artery at age 41. He also had complete occlusion of the superior mesenteric artery with compensatory flow through an enlarged and tortuous inferior mesenteric artery. He was homozygous for a previously identified FKBP14 mutation, c.362dupC, p.(Glu122Argfs*7). He had no mutations in COL3A1, ACTA2, TGFBR1, TGFBR2, or SMAD3. The FKBP14 mutations in our patient occurred on the same haplotype as others with this same mutation. Although one family member in a previous report was thought to have early vascular complications, it could not be confirmed that she had biallelic mutations in FKBP14. This report expands the phenotype of FKBP14‐related EDS to include risk for vascular complications and also raises the question of whether the shared haplotype represents a risk allele or founder mutation.

Endovascular Repair of Internal Mammary Artery Aneurysms in 2 Sisters with SMAD3 Mutation

True aneurysms of the internal mammary artery are rare and have been described in association with vasculitis or connective tissue disorders. Herein, we describe 2 cases of familial internal mammary artery aneurysms (IMAs) in 2 sisters with SMAD3 mutation. The older sister presented at the age of 54 years with an incidental diagnosis of a multilobed right IMA and the younger sister presented several years earlier with a ruptured left IMA aneurysm at the age of 49 years. Both sisters had Debakey type I aortic dissections prior to the IMA aneurysm presentation. To our knowledge, this is the first time IMA aneurysms have been described in siblings with SMAD3 mutation. In our experience, endovascular repair is a feasible and safe treatment option. An assessment of the entire arterial tree is recommended in patients diagnosed with SMAD3 mutations.