3137 fetuses in 33 years: What we have learned from the Wisconsin stillbirth service program.

The Wisconsin Stillbirth Service Program (WiSSP) provided expert review by a dysmorphologist for community-acquired data on 3137 fetal deaths between 1983 and 2017. Intrinsic fetal causes were consistently identified in about 25% while placental and maternal causes were recognized with increasing frequency as attention was shifted from a primarily fetal to a multifocal approach. Identification of causes increased from 40% to 78% and in about half of cases results of the review altered recurrence risk and/or future pregnancy management. Banked data from WiSSP formed the basis of 24 publications, more than half of which have a genetic counselor and/or summer premedical student intern as an author. The earlier publications emphasized validation of the concept of community-based evaluation with central review, the utility of various parts of the WiSSP protocol, the similarity of second-trimester miscarriages <20 weeks to later stillbirths with respect to causes identified and recurrence risks, and the potential for results of etiologic evaluation to influence future prenatal care. The most important recurrent theme, however, was the interaction of intrinsic fetal, placental, and maternal factors in contributing to fetal demise. This implies that, at least in developed nations with available obstetric care, reduction in stillbirth will require careful attention to the myriad of factors contributing to fetal, placental, and maternal well-being.

Pathogenic Mutations in Cancer-Predisposing Genes: A Survey of 300 Patients with Whole-Genome Sequencing and Lifetime Electronic Health Records.

BACKGROUND: It is unclear whether and how whole-genome sequencing (WGS) data can be used to implement genomic medicine. Our objective is to retrospectively evaluate whether WGS can facilitate improving prevention and care for patients with susceptibility to cancer syndromes. METHODS AND FINDINGS: We analyzed genetic mutations in 60 autosomal dominant cancer-predisposition genes in 300 deceased patients with WGS data and nearly complete long-term (over 30 years) medical records. To infer biological insights from massive amounts of WGS data and comprehensive clinical data in a short period of time, we developed an in-house analysis pipeline within the SeqHBase software framework to quickly identify pathogenic or likely pathogenic variants. The clinical data of the patients who carried pathogenic and/or likely pathogenic variants were further reviewed to assess their clinical conditions using their lifetime EHRs. Among the 300 participants, 5 (1.7%) carried pathogenic or likely pathogenic variants in 5 cancer-predisposing genes: one in APC, BRCA1, BRCA2, NF1, and TP53 each. When assessing the clinical data, each of the 5 patients had one or more different types of cancers, fully consistent with their genetic profiles. Among these 5 patients, 2 died due to cancer while the others had multiple disorders later in their lifetimes; however, they may have benefited from early diagnosis and treatment for healthier lives, had the patients had genetic testing in their earlier lifetimes. CONCLUSIONS: We demonstrated a case study where the discovery of pathogenic or likely pathogenic germline mutations from population-wide WGS correlates with clinical outcome. The use of WGS may have clinical impacts to improve healthcare delivery.

De novo mutations in NALCN cause a syndrome characterized by congenital contractures of the limbs and face, hypotonia, and developmental delay.

Freeman-Sheldon syndrome, or distal arthrogryposis type 2A (DA2A), is an autosomal-dominant condition caused by mutations in MYH3 and characterized by multiple congenital contractures of the face and limbs and normal cognitive development. We identified a subset of five individuals who had been putatively diagnosed with "DA2A with severe neurological abnormalities" and for whom congenital contractures of the limbs and face, hypotonia, and global developmental delay had resulted in early death in three cases; this is a unique condition that we now refer to as CLIFAHDD syndrome. Exome sequencing identified missense mutations in the sodium leak channel, non-selective (NALCN) in four families affected by CLIFAHDD syndrome. We used molecular-inversion probes to screen for NALCN in a cohort of 202 distal arthrogryposis (DA)-affected individuals as well as concurrent exome sequencing of six other DA-affected individuals, thus revealing NALCN mutations in ten additional families with "atypical" forms of DA. All 14 mutations were missense variants predicted to alter amino acid residues in or near the S5 and S6 pore-forming segments of NALCN, highlighting the functional importance of these segments. In vitro functional studies demonstrated that NALCN alterations nearly abolished the expression of wild-type NALCN, suggesting that alterations that cause CLIFAHDD syndrome have a dominant-negative effect. In contrast, homozygosity for mutations in other regions of NALCN has been reported in three families affected by an autosomal-recessive condition characterized mainly by hypotonia and severe intellectual disability. Accordingly, mutations in NALCN can cause either a recessive or dominant condition characterized by varied though overlapping phenotypic features, perhaps based on the type of mutation and affected protein domain(s).

SeqHBase: a big data toolset for family based sequencing data analysis.

BACKGROUND: Whole-genome sequencing (WGS) and whole-exome sequencing (WES) technologies are increasingly used to identify disease-contributing mutations in human genomic studies. It can be a significant challenge to process such data, especially when a large family or cohort is sequenced. Our objective was to develop a big data toolset to efficiently manipulate genome-wide variants, functional annotations and coverage, together with conducting family based sequencing data analysis. METHODS: Hadoop is a framework for reliable, scalable, distributed processing of large data sets using MapReduce programming models. Based on Hadoop and HBase, we developed SeqHBase, a big data-based toolset for analysing family based sequencing data to detect de novo, inherited homozygous, or compound heterozygous mutations that may contribute to disease manifestations. SeqHBase takes as input BAM files (for coverage at every site), variant call format (VCF) files (for variant calls) and functional annotations (for variant prioritisation). RESULTS: We applied SeqHBase to a 5-member nuclear family and a 10-member 3-generation family with WGS data, as well as a 4-member nuclear family with WES data. Analysis times were almost linearly scalable with number of data nodes. With 20 data nodes, SeqHBase took about 5 secs to analyse WES familial data and approximately 1 min to analyse WGS familial data. CONCLUSIONS: These results demonstrate SeqHBase's high efficiency and scalability, which is necessary as WGS and WES are rapidly becoming standard methods to study the genetics of familial disorders.

Mutations in PDGFRB cause autosomal-dominant infantile myofibromatosis.

Infantile myofibromatosis (IM) is a disorder of mesenchymal proliferation characterized by the development of nonmetastasizing tumors in the skin, muscle, bone, and viscera. Occurrence within families across multiple generations is suggestive of an autosomal-dominant (AD) inheritance pattern, but autosomal-recessive (AR) modes of inheritance have also been proposed. We performed whole-exome sequencing (WES) in members of nine unrelated families clinically diagnosed with AD IM to identify the genetic origin of the disorder. In eight of the families, we identified one of two disease-causing mutations, c.1978C>A (p.Pro660Thr) and c.1681C>T (p.Arg561Cys), in PDGFRB. Intriguingly, one family did not have either of these PDGFRB mutations but all affected individuals had a c.4556T>C (p.Leu1519Pro) mutation in NOTCH3. Our studies suggest that mutations in PDGFRB are a cause of IM and highlight NOTCH3 as a candidate gene. Further studies of the crosstalk between PDGFRB and NOTCH pathways may offer new opportunities to identify mutations in other genes that result in IM and is a necessary first step toward understanding the mechanisms of both tumor growth and regression and its targeted treatment.

Intestinal ganglioneuromatosis: unusual presentation of Cowden syndrome resulting in delayed diagnosis.

We report on a 25-year-old woman who presented as a teenager with macrocephaly and multiple gastrointestinal lesions including ganglioneuromas, hamartomas, lipomas, juvenile, and hyperplastic polyps in association with extra-intestinal tumors including a retroperitoneal lipoma, storiform collagenoma, and a fibrolipomatous hamartoma. PTEN mutation analysis identified a deletion in exon 2, confirming the diagnosis of Cowden syndrome. While intestinal polyps are common among Cowden patients who undergo endoscopy, and intestinal ganglioneuromas are occasionally reported, they are not usual presenting manifestations. Intestinal ganglioneuromatosis is divided into three subgroups: (1) polypoid ganglioneuromatosis (usually few isolated ganglioneuromas), (2) generalized ganglioneuromatosis (usually associated with NF1 or MEN), and (3) ganglioneuromatous polyposis without known systemic disease, although there are several reported patients with multiple lipomas. This individual with Cowden syndrome closely resembles the latter group, thus we suggest that patients with ganglioneuromatous polyposis, especially in association with lipomas, should be evaluated for possible Cowden syndrome.

Proximal microdeletions and microduplications of 1q21.1 contribute to variable abnormal phenotypes.

Chromosomal band 1q21.1 can be divided into two distinct regions, proximal and distal, based on segmental duplications that mediate recurrent rearrangements. Microdeletions and microduplications of the distal region within 1q21.1, which are susceptibility factors for a variety of neurodevelopmental phenotypes, have been more extensively studied than proximal microdeletions and microduplications. Proximal microdeletions are known as a susceptibility factor for thrombocytopenia-absent radius (TAR) syndrome, but it is unclear if these proximal microdeletions have other phenotypic consequences. Therefore, to elucidate the clinical significance of rearrangements of the proximal 1q21.1 region, we evaluated the phenotypes in patients identified with 1q21.1 rearrangements after referral for clinical microarray testing. We report clinical information for 55 probands with copy number variations (CNVs) involving proximal 1q21.1: 22 microdeletions and 20 reciprocal microduplications limited to proximal 1q21.1 and 13 microdeletions that include both the proximal and distal regions. Six individuals with proximal microdeletions have TAR syndrome. Three individuals with proximal microdeletions and two individuals with larger microdeletions of proximal and distal 1q21.1 have a 'partial' TAR phenotype. Furthermore, one subject with TAR syndrome has a smaller, atypical deletion, narrowing the critical deletion region for the syndrome. Otherwise, phenotypic features varied among individuals with these microdeletions and microduplications. The recurrent, proximal 1q21.1 microduplications are enriched in our population undergoing genetic testing compared with control populations. Therefore, CNVs in proximal 1q21.1 can be a contributing factor for the development of abnormal phenotypes in some carriers.

Patient and family experiences and opinions on adding 22q11 deletion syndrome to the newborn screen.

22q11 deletion syndrome (22qDS) has recently been proposed for addition to the newborn screening panel in Wisconsin and it seems likely that it may soon be considered in other states as well. Input from patients with 22qDS and their family was gathered from 21 phone interviews. Cardiac, palate, hypocalcemia, and multiple anomalies were common reasons for involved patients to be diagnosed, though age at diagnosis ranged from birth to adulthood. Many commented on their struggles with 22qDS, including worries about the future and the patient's independence. In general, respondents favored newborn screening for 22qDS because it would help prevent some medical problems, increase access to services, explain existing problems, and identify mild cases. However, a minority expressed reservations, including concerns that it would disrupt bonding, could be too costly, and would not be useful for mild cases.

Newborn screening programs: should 22q11 deletion syndrome be added?

The highly variable 22q11 deletion syndrome has been proposed for addition to newborn screening panels. A literature review investigated the incidence and prevalence, clinical features, and prognosis of 22q11 deletion syndrome and other issues related to newborn screening. Severe complications that could potentially be helped by screening include cardiac defects in 80% (with 20% having no outward signs to aid detection), hypocalcemia that can lead to seizures in 20% (though hypocalcemia is routinely investigated in sick newborns), and severe immune deficiency in <1% (which would be identified by some states' severe combined immunodeficiency screens). Other benefits that do not fit traditional goals of newborn screening include treatment for complications such as failure to thrive and developmental delay or preventing a "diagnostic odyssey." Although universal screening may prove the incidence to be >1:5000, undetected life-threatening effects occur in a minority of 22q11 deletion syndrome patients. Concerns include an untested screening technique, difficulty obtaining results in time for cardiac intervention, the chance of "vulnerable child syndrome" in mild cases, and possibly detecting congenital heart disease more efficiently by other means. Because addition of tests for highly variable conditions such as 22q11 deletion syndrome is likely to set a precedent for other syndromes, reevaluation of newborn screening criteria should be considered.

Janiceps conjoined twins with extreme asymmetry: case report with complete autopsy and histopathologic findings.

Conjoined twinning is a rare form of twinning, in which 2 bodies are attached, and is classified according to the anatomic place of attachment. An extremely rare form of conjoined twinning is janiceps conjoined twinning, in which 2 faces are attached but oriented in opposite directions. In this report, we present an unusual and difficult-to-classify case of conjoined male twins with partial duplication of craniofacial, upper oropharyngeal, and cardiac organs. We believe this to be one of the few reported cases of janiceps asymmetrus. We describe in detail the gross and microscopic pathology and offer some insights into the possible embryogenesis and distinction from the other rare form of conjoined twinning with facial duplication, diprosopus.

Variable outcomes in mosaic trisomy 16: five case reports and literature analysis.

OBJECTIVES: To report five cases of mosaic trisomy 16 with variable outcomes in the context of the literature on mosaic trisomy 16. Complications in these cases include preeclampsia, IUGR, fetal anomalies, and death, with no predictable pattern. METHODS: Observation of five new cases and statistical analysis of 125 reported cases of mosaic trisomy 16 with prenatal detection and outcome data. RESULTS: (1) IUGR, premature delivery, and/or physical anomalies are observed commonly, even when the trisomy is thought to be confined to the placenta; (2) Level II mosaicism for trisomy 16 in amniotic fluid may reflect a true mosaic state with phenotypic consequences; (3) FISH is more sensitive than traditional cytogenetics in detecting mosaicism in all tissue types examined; (4) hCG levels can be extremely elevated, and MS-AFP levels are often elevated; and (5) Uniparental disomy (UPD) increases the rates of IUGR and physical anomalies in CPM cases. CONCLUSION: While there is no obvious mosaic trisomy 16 syndrome, IUGR and heart defects commonly occur, even if the mosaicism appears to be confined to the placenta. A completely normal outcome occurs only in about 20% of the cases; however, complications can often be limited to prematurity, small-for-gestational-age infants, and/or minor or surgically reparable birth defects.