Next-generation sequencing for disorders of low and high bone mineral density.

UNLABELLED: To achieve an efficient molecular diagnosis of osteogenesis imperfecta (OI), Ehlers-Danlos syndrome (EDS), and osteopetrosis (OPT), we designed a next-generation sequencing (NGS) platform to sequence 34 genes. We validated this platform on known cases and have successfully identified the causative mutation in most patients without a prior molecular diagnosis. INTRODUCTION: Osteogenesis imperfecta, Ehlers-Danlos syndrome, and osteopetrosis are collectively common inherited skeletal diseases. Evaluation of subjects with these conditions often includes molecular testing which has important counseling and therapeutic and sometimes legal implications. Since several different genes have been implicated in these conditions, Sanger sequencing of each gene can be a prohibitively expensive and time-consuming way to reach a molecular diagnosis. METHODS: In order to circumvent these problems, we have designed and tested a NGS platform that would allow simultaneous sequencing on a single diagnostic platform of different genes implicated in OI, OPT, EDS, and other inherited conditions, leading to low or high bone mineral density. We used a liquid-phase probe library that captures 602 exons (~100 kb) of 34 selected genes and have applied it to test clinical samples from patients with bone disorders. RESULTS: NGS of the captured exons by Illumina HiSeq 2000 resulted in an average coverage of over 900X. The platform was successfully validated by identifying mutations in six patients with known mutations. Moreover, in four patients with OI or OPT without a prior molecular diagnosis, the assay was able to detect the causative mutations. CONCLUSIONS: In conclusion, our NGS panel provides a fast and accurate method to arrive at a molecular diagnosis in most patients with inherited high or low bone mineral density disorders.

Family history as a predictor of uptake of cancer preventive procedures by women with a BRCA1 or BRCA2 mutation.

Women with a BRCA1 or BRCA2 mutation are at an elevated risk of developing breast and ovarian cancer; however, it is unclear to what extent family history influences the uptake of cancer prevention options. Women with a BRCA1/2 mutation completed a follow-up questionnaire that assessed uptake of cancer preventive options. The pedigree of each woman was reviewed, and information was recorded on cancers diagnosed in relatives. Five hundred and seventeen women were included in the study. Women with a sister with breast cancer were more likely to have a prophylactic mastectomy than those without a sister with breast cancer [odds ratios (OR) = 2.4, p = 0.003]. Uptake of prophylactic mastectomy was significantly lower in women with a mother with ovarian cancer compared with those whose mother did not have ovarian cancer (OR = 0.4, p = 0.01). Having a mother or sister with ovarian cancer significantly predicted the uptake of prophylactic oophorectomy (OR = 1.6, p = 0.04). Women with a BRCA2 mutation were less likely to have a prophylactic oophorectomy than those with a BRCA1 mutation (OR = 0.49, p = 0.0004). Among women with a BRCA1 or BRCA2 mutation, family history predicts the uptake of prophylactic mastectomy and prophylactic oophorectomy.

Peripheral neuropathy in a child with Cree leukodystrophy.

The authors describe peripheral nerve involvement in a 12-month-old boy with Cree leukodystrophy. Nerve conduction and genetic studies were performed during investigation of his leukodystrophy. Mutation analysis of the eukaryotic initiation factor 2B5 gene detected homozygosity of the R195 mutation, confirming the diagnosis of Cree leukodystrophy. Median and posterior tibial motor nerve conduction study results were normal, but sensory responses in the median nerves were unobtainable bilaterally, in keeping with a sensory axonal neuropathy. Somatosensory-evoked potentials were absent in the upper extremities and delayed in the lower extremities, confirming sensory nerve involvement. This degree of sensory nerve involvement has not been previously reported in patients with eukaryotic initiation factor 2B5-related disorders. Peripheral neuropathy should be looked for both clinically and with electrodiagnostic studies in patients with eukaryotic initiation factor 2B-related disorders.

Chudley-McCullough syndrome: bilateral sensorineural deafness, hydrocephalus, and other structural brain abnormalities.

The Chudley-McCullough syndrome, an autosomal recessive condition first reported by Chudley et al. [1997], comprises profound sensorineural hearing loss and hydrocephalus secondary to an obstruction of the foramen of Munro. We describe two more sibs with this condition. One girl had sensorineural hearing loss and hydrocephalus due to obstruction of the foramen of Munro. Incidentally she was also found to carry a full mutation in the FMR1 gene. The older sister had profound sensorineural hearing loss and hydrocephalus not due to obstruction of the foramen of Munro; she also had callosal dysgenesis, gray matter heterotopia, cortical dysplasia, and cerebellar dysgenesis. Thus, the Chudley-McCullough syndrome may include hydrocephalus not necessarily related to obstruction of the foramen of Munro and other structural brain abnormalities.

Unusual phenotype in partial trisomy 14.

An 8-year-old boy with partial trisomy 14q and phenotype distinct from previously reported cases is described. The mother carries a balanced 9;14 reciprocal translocation. The patient presented with minor facial anomalies, developmental delay, hyperphagia, and obesity. Imprinting of maternal chromosome 14 or disruption of one or more genes on chromosome 9 may be responsible for our patient's manifestations.

SAMS: provisionally unique multiple congenital anomalies syndrome consisting of short stature, auditory canal atresia, mandibular hypoplasia, and skeletal abnormalities.

We report on a young Mennonite child born with short stature, atresia of the external auditory canal, mandibular hypoplasia, and skeletal anomalies. The skeletal defects consist of bilateral humeral hypoplasia, delayed ossification of the pubic rami, and the previously unreported anomaly of humeroscapular synostosis. This girl is the product of a consanguineous mating. This phenotype is unique and does not match that of any previously described condition.

A familial disorder with duodenal atresia and tetralogy of Fallot.

We report on two sibs with tetralogy of Fallot (TOF) and duodenal atresia (DA). The first child, a 6-year-old girl, had a right facial palsy in addition to the TOF and DA. Her brother, age 10 months, was born with bilateral microtia without facial palsy. The children are the product of an apparently non-consanguineous union between clinically normal parents. The pertinent family history includes a paternal aunt with TOF and a cleft lip and palate who died in childhood and another paternal aunt with a supernumerary thumb. This family has anomalies found in several syndromes, but does not meet the diagnostic criteria for any of them. The genetic basis for this condition remains unknown, but the pattern of inheritance is likely either autosomal recessive, or autosomal dominant with variable expression and reduced penetrance. The pathogenesis is unknown, but either a disturbance in neural crest cell migration or familial predisposition to vascular disruption might explain this pattern of malformations.

Two brothers with severe developmental delay, growth retardation and unusual appearance.

We report on two brothers with short stature, severe developmental delay and unusual appearance. Several conditions including the Russell-Silver, Dubowitz, Floating-Harbour and Cockayne syndromes were considered in the differential diagnosis, but subsequently rejected. These two cases are likely to represent a new autosomal recessive or X-linked recessive syndrome.

Clinical and neuroimaging findings of Cree leukodystrophy: a retrospective case series.

BACKGROUND AND PURPOSE: CLD is a rapidly progressive and invariably fatal neurodegenerative disorder. We describe clinical and neuroimaging findings in 5 infants with CLD. MATERIALS AND METHODS: Retrospective review of medical records of infants with CLD from the past 11 years at our institution was performed. Relevant clinical and demographic data were recorded. Specific attention was directed toward postmortem examination findings and genetic testing. CT and MR imaging results were reviewed. RESULTS: Five Cree infants were diagnosed with CLD. CT demonstrated bilateral symmetric hypoattenuation of the white matter and globus pallidus. MR imaging demonstrated corresponding T2 hyperintensity in these regions and abnormal signal intensity in the thalami and substantia nigra. Symmetric restricted diffusion in the deep white matter was seen. MRS demonstrated decreased NAA, elevated choline, and the presence of lactate. Postmortem examination in 1 infant showed corresponding poor myelination in the brain stem, cerebellum, deep gray structures, and the cerebral hemispheres. Genetic testing in 2 infants revealed homozygous mutations in the eIF2B5 gene. CONCLUSIONS: Neuroimaging in CLD is striking and is an important tool in diagnosing CLD. Extensive white matter involvement as well as involvement of the globus pallidus and patchy involvement of the thalami and substantia nigra are characteristic. MRS findings are compatible with destruction of normal brain parenchyma with evidence of anaerobic metabolism in the regions of demyelination. Clinical suspicion of VWM in a Native American infant from this region should prompt the consideration of CLD with appropriate imaging work-up and genetic testing.

Age at first birth and the risk of breast cancer in BRCA1 and BRCA2 mutation carriers.

An early age at first full-term birth is associated with a reduction in the subsequent development of breast cancer among women in the general population. A similar effect has not yet been reported among women who carry an inherited BRCA1 or BRCA2 mutation. We conducted a matched case-control study on 1816 pairs of women with a BRCA1 (n = 1405) or BRCA2 (n = 411) mutation in an attempt to elucidate the relationship between age at first full-term pregnancy and the risk of developing breast cancer. Information about the age at first childbirth and other pregnancy-related variables was derived from a questionnaire administered to women during the course of genetic counselling. There was no difference in the mean age at first full-term birth in the cases and controls (24.9 years vs. 24.8 years; P = 0.81, respectively). Compared to women whose first child was born at or before 18 years of age, a later age at first full-term birth did not influence the risk of developing breast cancer (OR = 1.00 per year; 95% CI 0.98-1.03; P-trend = 0.67). Stratification by mutation status did not affect the results. These findings suggest that an early first full-term birth does not confer protection against breast cancer in BRCA mutation carriers. Nonetheless, BRCA mutation carriers opting for a prophylactic oophorectomy as a breast and/or ovarian cancer risk-reducing strategy should complete childbearing prior to age 40 when this prevention modality is most effective.

Toy adaptations in pediatrics.

This report describes a special project of a Certified Occupational Therapy Assistant on a pediatric rehabilitation unit who learned to adapt battery operated toys for use by multihandicapped children. This led to the enhancement of patient treatment and requests for the assistant to consult with other professionals. Instructions are given for fabricating simple controls for use by handicapped children to activate battery operated toys.

A missense mutation in the oxi-3 gene of the [mi-3] extranuclear mutant of Neurospora crassa.

We have determined the DNA sequence of the oxi-3 gene and its 5' flanking region in the extranuclear [mi-3] mutant of Neurospora crassa. The oxi-3 gene encodes subunit 1 of cytochrome c oxidase, a protein known to be altered in the [mi-3] mutant (Bertrand, H., and Werner, S. (1979) Eur. J. Biochem. 98, 9-18). When the sequence from [mi-3] was compared to previously published sequences of the same region of mtDNA from wild-type N. crassa, a total of five differences was found. Four of these differences can be accounted for as either genetic polymorphisms or previous errors in DNA sequence determination. The remaining difference is a G/C to T/A transversion that changes a codon specifying an aspartic acid residue (GAC) to one that would specify tyrosine (TAC) at amino acid 448 of the 555 amino acid mature subunit 1 protein. This alteration was also found in the mtDNA of two separate heterokaryotic strains that had acquired the [mi-3] phenotype after repeated subculturing of heterokaryons forced between an [mi-3] strain and a strain containing a wild-type cytoplasm. The particular aspartic acid residue that would be affected by the mutation observed in [mi-3] is conserved in a diversity of species as either aspartic acid or glutamic acid, suggesting that an acidic residue at this position is important for the correct function of the subunit 1 protein. For these reasons, we consider it likely that the observed missense mutation is responsible for the [mi-3] phenotype.

The mitochondrial plasmid from Neurospora intermedia strain Labelle-1b contains a long open reading frame with blocks of amino acids characteristic of reverse transcriptases and related proteins.

We have determined the DNA sequence of the 4070 base pair mitochondrial plasmid from the Labelle-1b strain of Neurospora intermedia. Analysis of the sequence revealed that the plasmid contains a long open reading frame (ORF) that could encode a protein of up to 1151 amino acids. Codon usage in the long ORF shows no clear relationship to Neurospora mitochondrial genes, nuclear genes, nor to the ORF of a different Neurospora mitochondrial plasmid. The long ORF contains regions of similarity to yeast mitochondrial RNA polymerase as well as blocks of amino acids that are characteristic of reverse transcriptases and the ORFs of certain group II mtDNA introns (Michel and Lang, (1985) Nature 316,641). The plasmid gives rise to specific transcripts, some of which may be unit length, and which carry the information for expression of the long ORF. The genetic organization and content of the plasmid suggest that it is related to mobile genetic elements.

Construction of a DNA probe and detection of Actinobacillus pleuropneumoniae by using polymerase chain reaction.

A 1.5-kb Actinobacillus pleuropneumoniae 4074 DNA fragment from a genomic library was found to hybridization. No cross-hybridization hybridization. No cross-hybridization was detected with DNAs from hemolytic members of the family Pasteurellaceae. From the nucleotide sequence of the putative genomic probe, three primers were synthesized for use in polymerase chain reactions (PCRs), with 31 strains tested by using purified and crude DNA targets. PCR amplification products of 610 and 985 bp were observed in nucleic acids extracted from the 12 known serotypes and a biotype 2 strain. Template DNAs from other gram-negative and gram-positive bacteria, some of them found in the normal flora of swine and the upper respiratory tract, were not amplified by PCR. The only exception was an amplification of a similar 610- or 985-bp sequence in Actinobacillus lignieresii, a species that is closely related to A. pleuropneumoniae but that has never been isolated from swine. Amplification of specific A. pleuropneumoniae sequences by PCR directly from clinical specimens may find applications in the identification of asymptomatic carriers as well as in efforts to eradicate porcine pleuropneumonia.

Alteration of the cytochrome c oxidase subunit 2 gene in the [exn-5] mutant of Neurospora crassa.

The maternally inherited [exn-5] mutant of Neurospora crassa is characterized by its slow-growth rate and deficiency of cytochrome aa3 relative to wild-type strains. We have determined the DNA sequence of the COXI and COXII genes of the mutant, which encode subunits 1 and 2 of cytochrome c oxidase, respectively. No changes in the DNA sequence of the COXI gene relative to the corresponding wild-type gene were found. In the region of the COXII gene we found two alterations, one a C to T transition eight base pairs upstream of the coding sequence and the second within the coding sequence for subunit 2 affecting amino acid 27 of the precursor polypeptide (amino acid 15 of the mature polypeptide). The altered codon in [exn-5] specifies an isoleucine residue rather than the wild-type threonine residue. The corresponding position in subunit 2 sequences of all other organisms examined is conserved either as a threonine or a serine residue. Thus, we consider it likely that the mutation directly affecting the coding sequence of the polypeptide is responsible for the [exn-5] phenotype. Analysis of serially passaged heterokaryons constructed between wild-type and [exn-5] shows that both mutations segregate with the [exn-5] phenotype. Examination of mitochondrial translation products in [exn-5] revealed a deficiency of subunit 2, as well as the presence of a polypeptide that corresponds to a previously described precursor of subunit 1 that accumulates in a COXI mutant of N. crassa, [mi-3]. We propose possible relationships between [exn-5], [mi-3], and the nuclear su-1[mi-3] allele, which suppresses both mutations.

Mutations in the structural gene for cytochrome c result in deficiency of both cytochromes aa3 and c in Neurospora crassa.

The cyt-12-12 mutant of Neurospora crassa is characterized by slow growth and a deficiency of spectrophotometrically-detectable cytochromes aa3 and c. Using a sib-selection procedure we have isolated the cyt-12+ allele from a cosmid library of N. crassa genomic DNA. Characterization of the cyt-12+ allele reveals that it encodes the structural gene for cytochrome c. DNA sequence analysis of the cyt-12-12 allele revealed a mutation in the cytochrome c coding sequence that results in replacement of a glycine residue, which is invariant in the cytochrome c of other species, with an aspartic acid. Genetic analysis confirms that cyt-12-12 is allelic with the previously-characterized cyc-1-1 mutant, which was also shown to affect the single locus encoding cytochrome c in N. crassa. We suggest that the amount of functional cytochrome c present in mitochondria influences the level of cytochrome aa3.