Clinical Perspective on Use of Long-Read Sequencing in Prenatal Diagnosis of Thalassemia.

This is an editorial focusing on the clinical perspective of a long-read sequencing method in the prenatal diagnosis of alpha- and beta-thalassemia, including a comparison between this method and standard PCR-based methods. Though incremental, the increased sensitivity and specificity using long-read sequencing is an important advantage of this methodology in the prenatal diagnostic arena due to false positive or false negative results having greater consequence when a family is making decisions about their pregnancy.

Assessing deaf awareness training: knowledge and attitudes of recent genetic counseling graduates.

Research suggests that when healthcare providers lack cultural competence, minority groups, including the Deaf community, are adversely affected. Although most genetic counseling programs incorporate cultural competency training into their curricula, the extent and impact of Deaf awareness training is unknown. The purpose of this study is to assess Deaf awareness training of recent graduates and its impact on knowledge of deafness and Deaf culture, and attitudes toward deaf people. Genetic counselors who graduated within the past 5 years were invited to participate in an anonymous, online survey. Of the 135 respondents, 26 % reported no Deaf awareness training and 51 % reported limited training (1-2 h) conducted primarily by program instructors. Nearly one-third felt their Deaf awareness training was insufficient. Respondents lacked knowledge regarding effects of cochlear implants on residual hearing, communication between deaf children and hearing parents, and working with sign language interpreters. However, scores on knowledge of deafness and Deaf culture items and scores on attitudes toward deaf people scale did not differ significantly between respondents who had Deaf awareness training and those who did not. These findings suggest that genetic counseling students may not receive adequate Deaf awareness training. Future efforts should focus on increasing Deaf awareness in genetic counseling students, and investigating whether this change improves genetic counseling experiences for Deaf individuals.

Familial ebstein anomaly, left ventricular hypertrabeculation, and ventricular septal defect associated with a MYH7 mutation.

Ebstein anomaly is a rare congenital heart defect that most often occurs sporadically within a kindred. Familial cases, although reported, are uncommon. At this time, the genetic etiology of Ebstein anomaly is not fully elucidated. Here, we describe clinical and molecular investigations of a rare case of familial Ebstein anomaly in association with a likely pathogenic mutation of the MYH7 gene. The severity of presentation varies, and Ebstein anomaly can be observed in association with such other heart defects as ventricular septal defect and left ventricular (LV) hypertrabeculation, as seen in our family of study. In our family of study, the 31-year-old father and four of his children have been diagnosed with Ebstein anomaly. Genetic testing revealed that the father was heterozygous for the Glu1220del variant detected in exon 27 of the MYH7 gene. The MYH7 gene encodes the ß-myosin heavy chain and is expressed in cardiac muscle. DNA sequencing of three of his affected children confirmed that they carried the same variant while the fourth affected child was not available for testing. This is the first report of familial Ebstein anomaly associated with the Glu1220del mutation of the MYH7 gene. The mutation segregates with disease in a family with autosomal dominant transmission of congenital heart defects including Ebstein anomaly and other associated cardiovascular defects including LV hypertrabeculation and ventricular septal defect.

A synonymous variant in MYO15A enriched in the Ashkenazi Jewish population causes autosomal recessive hearing loss due to abnormal splicing.

Nonsyndromic hearing loss is genetically heterogeneous. Despite comprehensive genetic testing, many cases remain unsolved because the clinical significance of identified variants is uncertain or because biallelic pathogenic variants are not identified for presumed autosomal recessive cases. Common synonymous variants are often disregarded. Determining the pathogenicity of synonymous variants may improve genetic diagnosis. We report a synonymous variant c.9861 C > T/p.(Gly3287=) in MYO15A in homozygosity or compound heterozygosity with another pathogenic or likely pathogenic MYO15A variant in 10 unrelated families with nonsyndromic sensorineural hearing loss. Biallelic variants in MYO15A were identified in 21 affected and were absent in 22 unaffected siblings. A mini-gene assay confirms that the synonymous variant leads to abnormal splicing. The variant is enriched in the Ashkenazi Jewish population. Individuals carrying biallelic variants involving c.9861 C > T often exhibit progressive post-lingual hearing loss distinct from the congenital profound deafness typically associated with biallelic loss-of-function MYO15A variants. This study establishes the pathogenicity of the c.9861 C > T variant in MYO15A and expands the phenotypic spectrum of MYO15A-related hearing loss. Our work also highlights the importance of multicenter collaboration and data sharing to establish the pathogenicity of a relatively common synonymous variant for improved diagnosis and management of hearing loss.

Juvenile myelomonocytic leukemia-associated variants are associated with neo-natal lethal Noonan syndrome.

Gain-of-function variants in some RAS-MAPK pathway genes, including PTPN11 and NRAS, are associated with RASopathies and/or acquired hematological malignancies, most notably juvenile myelomonocytic leukemia (JMML). With rare exceptions, the spectrum of germline variants causing RASopathies does not overlap with the somatic variants identified in isolated JMML. Studies comparing these variants suggest a stronger gain-of-function activity in the JMML variants. As JMML variants have not been identified as germline defects and have a greater impact on protein function, it has been speculated that they would be embryonic lethal. Here we identified three variants, which have previously only been identified in isolated somatic JMML and other sporadic cancers, in four cases with a severe pre- or neo-natal lethal presentation of Noonan syndrome. These cases support the hypothesis that these stronger gain-of-function variants are rarely compatible with life.

Sources of fine particulate species in ambient air over lake Champlain Basin, VT.

This study is a part of an ongoing investigation of the types and locations of emission sources that contribute fine particulate air contaminants to Underhill, VT. The air quality monitoring data used for this study are from the Interagency Monitoring of Protected Visual Environments network for the period of 2001-2003 for the Underhill site. The main source-receptor modeling techniques used are the positive matrix factorization (PMF) and potential source contribution function (PSCF). This new study is intended as a comparison to a previous study of the 1988-1995 Underhill data that successfully revealed a total of 11 types of emission sources with significant contributions to this rural site. This new study has identified a total of nine sources: nitrate-rich secondary aerosol, wood smoke, East Coast oil combustion, automobile emission, metal working, soil/dust, sulfur-rich aerosol type I, sulfur-rich aerosol type II, and sea salt/road salt. Furthermore, the mass contributions from the PMF identified sources that correspond with sampling days with either good or poor visibility were analyzed to seek possible correlations. It has been shown that sulfur-rich aerosol type I, nitrate aerosol, and automobile emission are the most important contributors to visibility degradation. Soil/dust and sea salt/road salt also have an added effect.

Comprehensive diagnostic testing for stereocilin: an approach for analyzing medically important genes with high homology.

Next-generation sequencing (NGS) technologies have revolutionized genetic testing by enabling simultaneous analysis of unprecedented numbers of genes. However, genes with high-sequence homology pose challenges to current NGS technologies. Because diagnostic sequencing is moving toward exome analysis, knowledge of these homologous genes is essential to avoid false positive and negative results. An example is the STRC gene, one of >70 genes known to contribute to the genetic basis of hearing loss. STRC is 99.6% identical to a pseudogene (pSTRC) and therefore inaccessible to standard NGS methodologies. The STRC locus is also known to be a common site for large deletions. Comprehensive diagnostic testing for inherited hearing loss therefore necessitates a combination of several approaches to avoid pseudogene interference. We have developed a clinical test that combines standard NGS and NGS-based copy number assessment supplemented with a long-range PCR-based Sanger or MiSeq assay to eliminate pseudogene contamination. By using this combination of assays we could identify biallelic STRC variants in 14% (95% CI, 8%-24%) of individuals with isolated nonsyndromic hearing loss who had previously tested negative on our 70-gene hearing loss panel, corresponding to a detection rate of 11.2% (95% CI, 6%-19%) for previously untested patients. This approach has broad applicability because medically significant genes for many disease areas include genes with high-sequence homology.

NGS identifies TAZ mutation in a family with X-linked dilated cardiomyopathy.

We reported a family with two male siblings affected with infantile dilated cardiomyopathy (DCM). Extensive evaluation failed to identify the underlying cause for the DCM. Next generation sequencing (NGS) with targeted enrichment identified a hemizygous variant c.718G>C (p.Gly240Arg) in the TAZ gene. This variant has been reported in three other families with X linked infantile DCM and is therefore likely pathogenic. NGS allows efficient screening of a large number of uncommon genes in complex disorders like DCM, in which there is substantial genetic and phenotypic heterogeneity. The identification of TAZ mutation has major impact on their medical care as the surveillance needs to be expanded to cover for the Barth syndrome, a severe metabolic phenotype also caused by TAZ mutation, in addition to DCM.