Open-Source Artificial Intelligence System Supports Diagnosis of Mendelian Diseases in Acutely Ill Infants

Mendelian disorders are prevalent in neonatal and pediatric intensive care units and are a leading cause of morbidity and mortality in these settings. Current diagnostic pipelines that integrate phenotypic and genotypic data are expert-dependent and time-intensive. Artificial intelligence (AI) tools may help address these challenges. Dx29 is an open-source AI tool designed for use by clinicians. It analyzes the patient's phenotype and genotype to generate a ranked differential diagnosis. We used Dx29 to retrospectively analyze 25 acutely ill infants who had been diagnosed with a Mendelian disorder, using a targeted panel of ~5000 genes. For each case, a trio (proband and both parents) file containing gene variant information was analyzed, alongside patient phenotype, which was provided to Dx29 by three approaches: (1) AI extraction from medical records, (2) AI extraction with manual review/editing, and (3) manual entry. We then identified the rank of the correct diagnosis in Dx29's differential diagnosis. With these three approaches, Dx29 ranked the correct diagnosis in the top 10 in 92-96% of cases. These results suggest that non-expert use of Dx29's automated phenotyping and subsequent data analysis may compare favorably to standard workflows utilized by bioinformatics experts to analyze genomic data and diagnose Mendelian diseases.

SON-Related Zhu-Tokita-Takenouchi-Kim Syndrome With Recurrent Hemiplegic Migraine: Putative Role of PRRT2

Background and Objectives

Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome (OMIM 617140) is a recently identified neurodevelopmental disorder caused by heterozygous loss-of-function (LoF) variants in SON. Because the SON protein functions as an RNA-splicing regulator, it has been shown that some clinical features of ZTTK syndrome can be attributed to abnormal RNA splicing. Several neurologic features have been observed in patients with ZTTK syndrome, including seizure/epilepsy and other EEG abnormalities. However, a relationship between SON LoF in ZTTK syndrome and hemiplegic migraine remains unknown.

Methods

We identified a patient with a pathogenic variant in SON who shows typical clinical features of ZTTK syndrome and experienced recurrent episodes of hemiplegic migraine. To define clinical features, brain MRI and EEG during and after episodes of hemiplegic migraine were characterized. To identify molecular mechanisms for this clinical presentation, we investigated the impact of small interfering RNA (siRNA)-mediated SON knockdown on mRNA expression of the CACNA1A, ATP1A2, SCN1A, and PRRT2 genes, known to be associated with hemiplegic migraine, by quantitative RT-PCR. Pre-mRNA splicing of PRRT2 on SON knockdown was further examined by RT-PCR using primers targeting specific exons.

Results

Recurrent episodes of hemiplegic migraine in our patient typically followed modest closed head injuries, and recurrent seizures occurred during the most severe of these episodes. Transient hemispheric cortical interstitial edema and asymmetric EEG slowing were identified during episodes. Our siRNA experiments revealed that SON knockdown significantly reduces PRRT2 mRNA levels in U87MG and SH-SY5Y cell lines, although a reduction in CACNA1A, ATP1A2, and SCN1A mRNA expression was not observed. We further identified that SON knockdown leads to failure in intron 2 removal from PRRT2 pre-mRNA, resulting in a premature termination codon that blocks the generation of functionally intact full-length PRRT2.

Discussion

This report identifies recurrent hemiplegic migraine as a novel clinical manifestation of ZTTK syndrome, further characterizes this clinical feature, and provides evidence for downregulation of PRRT2 caused by SON LoF as a mechanism causing hemiplegic migraine. Examination of the SON gene may be indicated in individuals with recurrent hemiplegic migraine.

Multiple endocrine neoplasia type 2 (MEN2) and RET specific modifications of the ACMG/AMP variant classification guidelines and impact on the MEN2 RET database

The Multiple Endocrine Neoplasia type 2 (MEN2) RET proto-oncogene database, originally published in 2008, is a comprehensive repository of all publicly available RET gene variations associated with MEN2 syndromes. The variant-specific genotype/phenotype information, age of earliest reported medullary thyroid carcinoma (MTC) onset, and relevant references with a brief summary of findings are cataloged. The ACMG/AMP 2015 consensus statement on variant classification was modified specifically for MEN2 syndromes and RET variants using ClinGen sequence variant interpretation working group recommendations and ClinGen expert panel manuscripts, as well as manuscripts from the American Thyroid Association Guidelines Task Force on Medullary Thyroid Carcinoma and other MEN2 RET literature. The classifications for the 166 single unique variants in the MEN2 RET database were reanalyzed using the MEN2 RET specifically modified ACMG/AMP classification guidelines (version 1). Applying these guidelines added two new variant classifications to the database (likely benign and likely pathogenic) and resulted in clinically significant classification changes (e.g., from pathogenic to uncertain) in 15.7% (26/166) of the original variants. Of those clinically significant changes, the highest percentage of changes, 46.2% (12/26), were changes from uncertain to benign or likely benign. The modified ACMG/AMP criteria with MEN2 RET specifications will optimize and standardize RET variant classifications.

Survey of Meat Collected from Commercial Broiler Processing Plants Suggests Low Levels of Semicarbazide Can Be Created during Immersion Chilling

ABSTRACT

Semicarbazide (SEM) is routinely employed as an indicator for the use of nitrofurazone, a banned antimicrobial. The validity of SEM as a nitrofurazone marker has been scrutinized because of other possible sources of the compound. Nonetheless, a U.S. trade partner rejected skin-on chicken thighs because of SEM detection and suspected nitrofurazone use. Because nitrofurazone has been banned in U.S. broiler production since 2003, we hypothesized that incidental de novo SEM formation occurs during broiler processing. To assess this possibility, raw leg quarters were collected from 23 commercial broiler processing plants across the United States and shipped frozen to our laboratory, where liquid chromatography-mass spectrometry was used to quantitatively assess for SEM. Leg quarter samples were collected at four points along the processing line: hot rehang (transfer from the kill line to the evisceration line), prechill (before the chilling process), postchill (immediately following chilling), and at the point of pack. Thigh meat with skin attached was removed from 535 leg quarters and analyzed in triplicate for SEM concentrations. The concentrations ranged from 0 to 2.67 ppb, with 462 (86.4%) of 535 samples below the regulatory decision level of 0.5 ppb of SEM. The 73 samples over the 0.5-ppb limit came from 21 plants; 53 (72.6%) of positive samples were in meat collected after chilling (postchill or point of pack). The difference in both prevalence and concentration of SEM detected before and after chilling was highly significant (P < 0.0001). These data support our hypothesis that SEM detection in raw broiler meat is related to de novo creation of the chemical during processing.

HIGHLIGHTS

Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia

BACKGROUND

Genetic disorders contribute to significant morbidity and mortality in critically ill newborns. Despite advances in genome sequencing technologies, a majority of neonatal cases remain unsolved. Complex structural variants (SVs) often elude conventional genome sequencing variant calling pipelines and will explain a portion of these unsolved cases.

METHODS

As part of the Utah NeoSeq project, we used a research-based, rapid whole-genome sequencing (WGS) protocol to investigate the genomic etiology for a newborn with a left-sided congenital diaphragmatic hernia (CDH) and cardiac malformations, whose mother also had a history of CDH and atrial septal defect.

RESULTS

Using both a novel, alignment-free and traditional alignment-based variant callers, we identified a maternally inherited complex SV on chromosome 8, consisting of an inversion flanked by deletions. This complex inversion, further confirmed using orthogonal molecular techniques, disrupts the ZFPM2 gene, which is associated with both CDH and various congenital heart defects.

CONCLUSIONS

Our results demonstrate that complex structural events, which often are unidentifiable or not reported by clinically validated testing procedures, can be discovered and accurately characterized with conventional, short-read sequencing and underscore the utility of WGS as a first-line diagnostic tool.

Pointing in a different direction: a case of bilateral absence of extensor indicis

Understanding anatomical variations, as well as, normal anatomy of the muscles and tendons of the hand is vital for successful clinical evaluation and surgery. A number of extensor muscle and tendon variations have been reported in the literature including duplication, triplication, and absence. We report a rare anatomical variation that includes bilateral absence of the extensor indicis (EI) muscles and bilateral duplication of the extensor digitorum (ED) tendon to the second digit in the forearm of an 83-year-old male cadaver during routine upper limbs dissection. In the present case, only three muscles were present in the deep compartment: extensor pollicis longus (EPL), extensor pollicis brevis (EPB), and abductor pollicis longus (APL) with bilateral absence of EI. The reported prevalence of bilateral absence of EI muscle and tendon ranges from 0.5 to 3.5% [1, 26]. The prevalence of an additional index tendon arising bilaterally from the ED muscle belly is 3.2 % of the population [1]. Extension of the index finger is governed by the actions of EI and ED. However, the four tendons of ED are linked to each other by juncturae tendinum (JT), restricting independent extension of the digits in certain postures, e.g. when the hand is fisted. With fisted hand, EI controls extension of the index finger. Clinically, EI tendons are used for tendon reconstruction procedures to restore function to the hand and thumb after trauma or tendon rupture. This report highlights the importance of anticipating anatomical variations and conducting pre-operative evaluations to confirm the presence of EI when planning tendon transfer procedures.

Evaluation of internet derived patient information for Acute Pancreatitis

INTRODUCTION

Possibly In the UK there are currently over 26,000 patients admitted to hospital for acute pancreatitis per annum and the incidence is rising. 55% of patients consult the internet for information regarding their medical condition. As the number of people using the internet has increased 57% since 2006, it is increasingly important for medical professionals to direct patients to accurate online sources of information. This paper aims to evaluate the quality of information available online for acute pancreatitis.

METHODS

The term 'acute pancreatitis' was searched using http://www.google.com, http://www.bing.com, and http://www.yahoo.com. The top 10 results of each of these websites were assessed using the University of Michigan consumer health website evaluation checklist.

RESULTS

Of the 30 websites found, 4 were excluded from the evaluation. Within the 26 evaluated websites there was high variability in website quality. However, the authors would have used 18 of the websites again for the purpose of finding out information on acute pancreatitis. 15 websites had a named author of which 11 displayed their credentials. 8 of the websites had been updated within the last year. 10 websites displayed a bias or conflict of interest. Generally, the layout and design of websites was good, however 7 of the websites contained distracting graphics and 9 of the websites had no search facility.

DISCUSSION

Doctors should give patients the information they want and need. With a high percentage of patients using the internet, medical professionals should recommend good quality websites to their patients. Engaging in this process could improve the consenting process as patients would be better informed. Good quality websites allows patients to explore conditions by themselves, with a re-consultation facilitating further discussion. Failure to engage in internet-based information risks patients making misinformed decisions due to bias and conflict of interest.

Assessing clinical education tools for expanded carrier screening

Expanded carrier screening (ECS) is increasingly offered to a broader population and raises challenges of how to best educate and counsel the volume of screened individuals. For this study, we compared three educational tools (brochure, video and comic) about ECS on knowledge and decision making. A convenience online sample of 151 pregnant women was randomized to one of three groups (Video, n = 42; Comic n = 54; Brochure n = 55). Knowledge scores were significantly higher for the comic group compared to the video or the brochure groups (p < .001). No significant differences in preparation for decision making, decisional conflict, or perceptions of shared decision making were identified between the study groups. This study suggests that a comic about ECS may improve patient attention and retention of information. The use of graphic narratives may enable individuals to better understand medical information in general.

De novo variants in PAK1 lead to intellectual disability with macrocephaly and seizures

Using trio exome sequencing, we identified de novo heterozygous missense variants in PAK1 in four unrelated individuals with intellectual disability, macrocephaly and seizures. PAK1 encodes the p21-activated kinase, a major driver of neuronal development in humans and other organisms. In normal neurons, PAK1 dimers reside in a trans-inhibited conformation, where each autoinhibitory domain covers the kinase domain of the other monomer. Upon GTPase binding via CDC42 or RAC1, the PAK1 dimers dissociate and become activated. All identified variants are located within or close to the autoinhibitory switch domain that is necessary for trans-inhibition of resting PAK1 dimers. Protein modelling supports a model of reduced ability of regular autoinhibition, suggesting a gain of function mechanism for the identified missense variants. Alleviated dissociation into monomers, autophosphorylation and activation of PAK1 influences the actin dynamics of neurite outgrowth. Based on our clinical and genetic data, as well as the role of PAK1 in brain development, we suggest that gain of function pathogenic de novo missense variants in PAK1 lead to moderate-to-severe intellectual disability, macrocephaly caused by the presence of megalencephaly and ventriculomegaly, (febrile) seizures and autism-like behaviour.

Abstract 558: MERTK-specific antibodies that have therapeutic antitumor activity in mice disrupt the integrity of the retinal pigmented epithelium in cynomolgus monkeys

MERTK, a member of the TAM (TYRO3, AXL, MERTK) family of receptor tyrosine kinases, is a pleiotropic immune modulator that controls efferocytosis. Engagement of MERTK with its ligand GAS6, found anchored to phosphatidylserine exposed on the outer membrane of apoptotic cells, triggers MERTK phosphorylation and signaling events that culminate in the removal of apoptotic debris. Recent studies have highlighted the expression of MERTK on tumor-associated macrophages, and Mertk-deficient mice show reduced tumor cell growth accompanied by inflammatory cytokine production and alterations in macrophage activation. Thus, MERTK has emerged as a promising therapeutic target for augmenting innate antitumor immune responses. MERTK is also expressed in retinal pigmented epithelium (RPE) cells of the eye where it mediates phagocytosis of photoreceptor outer segment fragments. Mutations in MERTK that disrupt its expression or kinase activity lead to marked retinal degeneration and blindness in mice, rats, and humans. Due to known differences in blood-retinal permeability, we explored whether therapeutic antibodies targeting MERTK could inhibit macrophage-mediated efferocytosis and promote antitumor activity while sparing RPE toxicity. A diverse panel of high-affinity antibodies was developed to explore MERTK blockade in vitro and in vivo. Multiple antibodies disrupted MERTK-GAS6 binding and blocked human and murine macrophage-mediated efferocytosis. Two antibodies targeting distinct GAS6 binding epitopes were selected for further characterization. Both antibodies demonstrated antitumor activity in murine CT26 and MC38 syngeneic colorectal cancer models and led to alterations in immune cell-related gene expression. To investigate potential effects on RPE biology with MERTK antibodies, a multi-dose, 4-week cynomolgus monkey study with several in-life and post-mortem ophthalmologic endpoints was designed. While no abnormal ophthalmic or electroretinography (ERG) findings were detected, all animals treated with either MERTK antibody at all doses showed histological abnormalities of the retina, including vacuolation of the outer segments of photoreceptors, displacement of RPE cells, and single cell necrosis of the outer nuclear layer. These data suggest that inhibition of efferocytosis by antibody-mediated blockade of MERTK can promote immune activation and inhibit tumor growth in vivo; however, retinal toxicity consistent with histological observations made in Mertk mutant animals is an on-target effect. As several therapeutics that block MERTK function are currently in preclinical development, a thorough evaluation of retinal toxicity is warranted.

Citation Format: Kerry F. White, Matthew Rausch, Jing Hua, Katherine H. Walsh, Christine E. Miller, Christopher C. Wells, Devapregasan Moodley, Benjamin H. Lee, Scott C. Chappel, Pamela M. Holland, Jonathan A. Hill. MERTK-specific antibodies that have therapeutic antitumor activity in mice disrupt the integrity of the retinal pigmented epithelium in cynomolgus monkeys [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 558.

Targeted gene panel sequencing for the rapid diagnosis of acutely ill infants

Background

Exome/genome sequencing (ES/GS) have been recently used in neonatal and pediatric/cardiac intensive care units (NICU and PICU/CICU) to diagnose and care for acutely ill infants, but the effectiveness of targeted gene panels for these purposes remains unknown.

Methods

RapSeq, a newly developed panel targeting 4,503 disease‐causing genes, was employed on selected patients in our NICU/PICU/CICU. Twenty trios were sequenced from October 2015 to March 2017. We assessed diagnostic yield, turnaround times, and clinical consequences.

Results

A diagnosis was made in 10/20 neonates (50%); eight had de novo variants (ASXL1, CHD, FBN1, KMT2D, FANCB, FLNA, PAX3), one was a compound heterozygote for CHAT, and one had a maternally inherited GNAS variant. Preliminary reports were generated by 9.6 days (mean); final reports after Sanger sequencing at 16.3 days (mean). In all positive infants, the diagnosis changed management. In a case with congenital myasthenia, diagnosis and treatment occurred at 17 days versus 7 months in a historical control.

Conclusions

This study shows that a gene panel that includes the majority of known disease‐causing genes can rapidly identify a diagnosis in a large number of tested infants. Due to simpler deployment and interpretation and lower costs, this approach might represent an alternative to ES/GS in the NICU/PICU/CICU.

Novel mutation in CCBE 1 as a cause of recurrent hydrops fetalis from Hennekam lymphangiectasia-lymphedema syndrome-1

Whole exome sequencing (WES) was used to determine the etiology of recurrent hydrops fetalis in this case of Hennekam lymphangiectasia-lymphedema syndrome-1. WES is a useful approach for diagnosing rare single-gene conditions with nonspecific phenotypes and should be considered early in the diagnostic process of investigating fetal abnormalities.

The Controlled Palatal Harvest (CPH) Technique for Harvesting a Palatal Subepithelial Connective Tissue Graft

The use of methamphetamines is a significant public health concern not only in America but worldwide. The consequences of this drug's use are widespread, having major physiologic and psychological effects that are damaging to users' bodies and well-being. Meth use wreaks havoc on one's oral health, with the effects including demineralization of tooth surfaces, carious lesions, inflammation of the periodontium, and more. In addition to examining the neurotoxic effects that methamphetamines have on the brain, this article will discuss how dental professionals can approach treatment of individuals who are affected by this debilitating drug, utilizing a strategy that combines caries arrest with oral hygiene improvement and disease prevention. It will also review the use of various products to help establish a neutral oral pH and enhance enamel remineralization.

Reporting incidental findings in genomic scale clinical sequencing--a clinical laboratory perspective: a report of the Association for Molecular Pathology

Advances in sequencing technologies have facilitated concurrent testing for many disorders, and the results generated may provide information about a patient's health that is unrelated to the clinical indication, commonly referred to as incidental findings. This is a paradigm shift from traditional genetic testing in which testing and reporting are tailored to a patient's specific clinical condition. Clinical laboratories and physicians are wrestling with this increased complexity in genomic testing and reporting of the incidental findings to patients. An enormous amount of discussion has taken place since the release of a set of recommendations from the American College of Medical Genetics and Genomics. This discussion has largely focused on the content of the incidental findings, but the laboratory perspective and patient autonomy have been overlooked. This report by the Association of Molecular Pathology workgroup discusses the pros and cons of next-generation sequencing technology, potential benefits, and harms for reporting of incidental findings, including the effect on both the laboratory and the patient, and compares those with other areas of medicine. The importance of genetic counseling to preserve patient autonomy is also reviewed. The discussion and recommendations presented by the workgroup underline the need for continued research and discussion among all stakeholders to improve our understanding of the effect of different policies on patients, providers, and laboratories.

High-throughput synchrotron X-ray diffraction for combinatorial phase mapping

Discovery of new materials drives the deployment of new technologies. Complex technological requirements demand precisely tailored material functionalities, and materials scientists are driven to search for these new materials in compositionally complex and often non-equilibrium spaces containing three, four or more elements. The phase behavior of these high-order composition spaces is mostly unknown and unexplored. High-throughput methods can offer strategies for efficiently searching complex and multi-dimensional material genomes for these much needed new materials and can also suggest a processing pathway for synthesizing them. However, high-throughput structural characterization is still relatively under-developed for rapid material discovery. Here, a synchrotron X-ray diffraction and fluorescence experiment for rapid measurement of both X-ray powder patterns and compositions for an array of samples in a material library is presented. The experiment is capable of measuring more than 5000 samples per day, as demonstrated by the acquisition of high-quality powder patterns in a bismuth-vanadium-iron oxide composition library. A detailed discussion of the scattering geometry and its ability to be tailored for different material systems is provided, with specific attention given to the characterization of fiber textured thin films. The described prototype facility is capable of meeting the structural characterization needs for the first generation of high-throughput material genomic searches.

Genetic counselor review of genetic test orders in a reference laboratory reduces unnecessary testing

Genetic tests are routinely ordered by health care providers (HCPs) within a wide range of medical specialties. Many providers have limited knowledge or experience with ordering and interpreting genetic tests; thus, test order errors are common. Rigorous review of genetic test orders by genetic counselors (GCs) can provide a direct financial benefit to medical institutions, patients and insurers. GCs at ARUP (Associated Regional University Pathologists) Laboratories routinely perform a preanalytic assessment of complex molecular genetic test orders that includes reviewing clinical and family history information and considering the clinical utility and cost-effectiveness of ordered tests. GCs contact the ordering institution and/or HCP as needed to collect additional clinical information and confirm the test order or suggest alternative testing based on the provided information. A retrospective review of the GC-facilitated test changes over a 21-month period at ARUP laboratories was performed. Approximately 26% of all requests for complex genetic tests assessing germ line mutations were changed following GC review. Testing fees associated with canceled tests were summed to estimate the cost-savings resulting from GC-facilitated test reviews. The test review process resulted in an average reduction in charges to the referring institutions of $48,000.00 per month. GC review of genetic test orders for appropriateness and clinical utility reduces healthcare costs to hospitals, insurers, and patients.

Triplet repeat primed PCR simplifies testing for Huntington disease

Diagnostic and predictive testing for Huntington disease (HD) requires an accurate determination of the number of CAG repeats in the Huntingtin (HHT) gene. Currently, when a sample appears to be homozygous for a normal allele, additional testing is required to confirm amplification from both alleles. If the sample still appears homozygous, Southern blot analysis is performed to rule out an undetected expanded HTT allele. Southern blot analysis is expensive, time-consuming, and labor intensive and requires high concentrations of DNA. We have developed a chimeric PCR process to help streamline workflow; true homozygous alleles are easily distinguished by this simplified method, and only very large expanded alleles still require Southern blot analysis. Two hundred forty-six HD samples, previously run with a different fragment analysis method, were analyzed with our new method. All samples were correctly genotyped, resulting in 100% concordance between the methods. The chimeric PCR assay was able to identify expanded alleles up to >150 CAG repeats. This method offers a simple strategy to differentiate normal from expanded CAG alleles, thereby reducing the number of samples reflexed to Southern blot analysis. It also provides assurance that expanded alleles are not routinely missed because of allele dropout.

Implementation of a cost-effective unlabeled probe high-resolution melt assay for genotyping of Factor V Leiden

The Factor V Leiden mutation (FVL; c.1601G>A, p.Arg534Gln), the most common aberration underlying activated Protein C resistance, results in disruption of a major anticoagulation pathway and is a leading cause of inherited thrombophilia. A high-throughput assay for FVL mutation detection was developed using a single unlabeled probe on a high-resolution platform, the 96-well Roche 480 LightCycler (LC480) instrument. This method replaced the U.S. Food and Drug Administration-approved Roche Factor V Leiden kit assay on the LightCycler PCR instrument, decreasing total cost by 48%. The analytical sensitivity and specificity of the LC480 high-resolution assay approached 100% for the FVL mutation. Factor V mutations in proximity to the FVL locus may influence probe binding efficiency and melt characteristics. One out of three very rare variants tested in a separate study, 1600delC, was not distinguishable from FVL using the described high-resolution assay. However, a c.1598G>A variant, which changes the amino acid sequence from arginine to lysine at position 533, was detected by this high-resolution assay and confirmed by bidirectional sequencing. In the labeled probe LightCycler assay, the c.1598G>A variant was indistinguishable from the heterozygous FVL control. The c.1598G>A variant has not been described previously and its clinical significance is uncertain. In conclusion, the LC480 FVL assay is cost effective in a high-throughput setting, with capability to detect both previously described and novel FV variants.

Clinical analysis of PMS2: mutation detection and avoidance of pseudogenes

Germline mutation detection in PMS2, one of four mismatch repair genes associated with Lynch syndrome, is greatly complicated by the presence of numerous pseudogenes. We used a modification of a long-range PCR method to evaluate PMS2 in 145 clinical samples. This modification avoids potential interference from the pseudogene PMS2CL by utilizing a long-range product spanning exons 11-15, with the forward primer anchored in exon 10, an exon not shared by PMS2CL. Large deletions were identified by MLPA. Pathogenic PMS2 mutations were identified in 22 of 59 patients whose tumors showed isolated loss of PMS2 by immunohistochemistry (IHC), the IHC profile most commonly associated with a germline PMS2 mutation. Three additional patients with pathogenic mutations were identified from 53 samples without IHC data. Thirty-seven percent of the identified mutations were large deletions encompassing one or more exons. In 27 patients whose tumors showed absence of either another protein or combination of proteins, no pathogenic mutations were identified. We conclude that modified long-range PCR can be used to preferentially amplify the PMS2 gene and avoid pseudogene interference, thus providing a clinically useful germline analysis of PMS2. Our data also support the use of IHC screening to direct germline testing of PMS2.

Detection of large rearrangements in the cystic fibrosis transmembrane conductance regulator gene by multiplex ligation-dependent probe amplification assay when sequencing fails to detect two disease-causing mutations

AIMS

Most of the over 1600 mutations and sequence variants identified to date in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are point mutations or small deletions/insertions detectable by conventional sequencing. However, large rearrangements (deletions, duplications, or insertion/deletion mutations) have recently been reported to constitute 1-2% of CFTR mutations. The CFTR sequencing protocol at ARUP Laboratories interrogates the coding regions of all 27 exons and all intron/exon boundaries of the gene. This study was undertaken to determine whether testing for large gene rearrangements could improve the mutation detection rate.

RESULTS

Nine cases with abnormal quantitative pilocarpine iontophoresis sweat chloride (SC) values (>60 mEq/L) and 20 cases with borderline SC levels (40-60 mEq/L) with only one or no mutations detected by the ARUP 32 mutation panel, including the 23 mutations recommended by American College of Medical Genetics (ACMG) for carrier screening, followed by sequencing, were tested using a multiplex ligation-dependent probe amplification (MLPA) assay. MLPA analysis identified one deletion among nine patients with SC >60 who had previously been tested with sequencing. None of the cases with borderline SC levels showed rearrangements.

CONCLUSION

The MLPA assay for detection of large rearrangements may be valuable in individuals with positive SC levels where one or no mutations have been identified by sequencing.

L-Glutamic acid as a mediator of sexual morphogenesis in Volvox capensis

In Volvox capensis the development of sexual individuals is in response to low concentrations (68 nM) of L-glutamic acid rather than to such species-specific glycoproteins as have been isolated in Volvox carteri or are believed to exist in a number of other species. V. capensis grows equally as well in light and in darkness in a medium supplemented with sodium acetate; however, L-glutamic acid is active as an inducer of the sexual form only in populations grown in the light. The site of action of L-glutamic acid and its biochemical role in the sexual response are unknown. Attempts to induce the sexual response by using the other L-amino acids, various analogs of glutamic acid, compounds of similar structure (e.g., gamma-aminobutyric acid), and intermediates of biochemical pathways known to involve L-glutamic acid (e.g., alpha-ketoglutarate or pyroglutamic acid) have been unsuccessful. L-Glutamic acid is produced by V. capensis as a natural product of the digestion of the glycoproteinaceous parental matrix at the time young spheroids escape. As a population increases, so does the level of L-glutamic acid produced at each succeeding generation until the threshold of sensitivity is reached and the induction of sexual forms is effected. This serves as a mechanism for ensuring the production of sexual spheroids and their zygotes, the only phase in the life cycle resistant to drying. Thus, Volvox is especially adapted to an existence in ephemeral pools of water resulting from seasonal rains.

Structure and orientational texture of self-organizing lipid bilayers

The structure of single supported dipalmitoyl-phosphatidylcholine bilayers prepared by vesicle fusion or Langmuir-Blodgett-Schaeffer (LBS) deposition techniques was characterized by x-ray reflectivity and grazing incidence diffraction in bulk water. LBS bilayers display symmetric leaflets similar to monolayer structures, while vesicle fusion yields more inhomogeneous bilayers. Diffraction establishes that lipids are always coupled across the bilayer even when leaflets are deposited independently and suggests the existence of orientational texture.

Ontogenetic scaling of foot musculoskeletal anatomy in elephants

This study quantifies the shape change in elephant manus and pes anatomy with increasing body mass, using computed tomographic scanning. Most manus and pes bones, and manus tendons, maintain their shape, or become more gracile, through ontogeny. Contrary to this, tendons of the pes become significantly more robust, suggesting functional adaptation to increasingly high loads. Ankle tendon cross-sectional area (CSA) scales the highest in the long digital extensor, proportional to body mass(1.08+/-0.21), significantly greater than the highest-scaling wrist tendon (extensor carpi ulnaris, body mass(0.69+/-0.09)). These patterns of shape change relate to the marked anatomical differences between the pillar-like manus and tripod-like pes, consistent with differences in fore- and hindlimb locomotor function. The cartilaginous predigits (prepollux and prehallux) of the manus and pes also become relatively more robust through ontogeny, and their pattern of shape change does not resemble that seen in any of the 10 metacarpals and metatarsals. Their CSAs scale above isometry proportional to body mass(0.73+/-0.09) and body mass(0.82+/-0.07) respectively. We infer a supportive function for these structures, preventing collapse of the foot pad during locomotion.

Probing the local order of single phospholipid membranes using grazing incidence x-ray diffraction

We report the first grazing incidence x-ray diffraction measurements of a single phospholipid bilayer at the solid-liquid interface. Our grazing incidence x-ray diffraction and reflectivity measurements reveal that the lateral ordering in a supported DPPE (1, 2-Dipalmitoyl-sn-Glycero-3-Phosphoethanolamine) bilayer is significantly less than that of an equivalent monolayer at the air-liquid interface. Our findings also indicate that the leaflets of the bilayer are uncoupled in contrast to the scattering from free standing phosphatidylcholine bilayers. The methodology presented can be readily implemented to study more complicated biomembranes and their interaction with proteins.

Selection of a Microbiological Corrosion System for Studying Effects on Structural Aluminum Alloys

Two laboratory methods, a metal-strip test and a tank test, were evaluated as microbiological corrosion systems for producing corroded test specimens on a structural aluminum alloy. The results show that corrosion of the test alloy occurred best in the metal-strip test in a deionized water-fuel medium inoculated with a mixture of microorganisms under aerated conditions. The metal-strip test was more successful for producing large numbers of corroded test specimens and proved more economical than the tank-type test, since less structural material is needed to obtain a specimen with sufficient corrosion areas, and since the corrosion can more easily be restricted by maskants to certain areas for specific test purposes.

Access to care for people with special needs: role of alternative providers and practice settings

Oral Health in America: A Report of the Surgeon General released in 2000 was the first-ever surgeon general's report on the status of oral health in the United States. It clearly outlined a growing set of challenges in such areas as reducing oral health disparities, improving access to oral and dental care, and prevention of common dental diseases. Findings revealed that 75 percent of dental disease is found in 25 percent of the population. California's children have twice as much untreated decay as their national counterparts. For children with special health care needs seeing a dentist, the data is sparse but a survey of general dentists conducted in 2001 showed that only 10 percent see these children often or very often.

Characterization of biological thin films at the solid-liquid interface by x-ray reflectivity

We demonstrate that 18 keV x-rays can be used to study organic thin films at the solid-liquid interface by x-ray reflectivity. We establish that this is a powerful technique for investigating biological systems in a previously inaccessible manner. Our measurements enabled the density distribution of single phospholipid bilayer membranes in bulk water to be measured with unprecedented precision. Previously, characterization of biomimetic structures normal to a "buried" interface was a domain of neutron reflectivity.

Confocal imaging of the embryonic heart: how deep?

Confocal microscopy allows for optical sectioning of tissues, thus obviating the need for physical sectioning and subsequent registration to obtain a three-dimensional representation of tissue architecture. However, practicalities such as tissue opacity, light penetration, and detector sensitivity have usually limited the available depth of imaging to 200 microm. With the emergence of newer, more powerful systems, we attempted to push these limits to those dictated by the working distance of the objective. We used whole-mount immunohistochemical staining followed by clearing with benzyl alcohol-benzyl benzoate (BABB) to visualize three-dimensional myocardial architecture. Confocal imaging of entire chick embryonic hearts up to a depth of 1.5 mm with voxel dimensions of 3 microm was achieved with a 10x dry objective. For the purpose of screening for congenital heart defects, we used endocardial painting with fluorescently labeled poly-L-lysine and imaged BABB-cleared hearts with a 5x objective up to a depth of 2 mm. Two-photon imaging of whole-mount specimens stained with Hoechst nuclear dye produced clear images all the way through stage 29 hearts without significant signal attenuation. Thus, currently available systems allow confocal imaging of fixed samples to previously unattainable depths, the current limiting factors being objective working distance, antibody penetration, specimen autofluorescence, and incomplete clearing.

Neutron and X-ray scattering studies of cholera toxin interactions with lipid monolayers at the air–liquid interface

Using neutron/X-ray reflectivity and X-ray grazing incidence diffraction (GID), we have characterized the structure of mixed DPPE:GM(1) lipid monolayers before and during the binding of cholera toxin (CTAB(5)) or its B subunit (CTB(5)). Structural parameters such as the density and thickness of the lipid layer, extension of the GM(1) oligosaccharide headgroup, and orientation and position of the protein upon binding are reported. Both CTAB(5) and CTB(5) were measured to have approximately 50% coverage when bound to the lipid monolayer. X-ray GID experiments show that both the lipid monolayer and the cholera toxin layer are crystalline. The effects of X-ray beam damage have been assessed and the monolayer/toxin structure does not change with time after protein binding has saturated.

Cholera toxin assault on lipid monolayers containing ganglioside GM1

Many bacterial toxins bind to and gain entrance to target cells through specific interactions with membrane components. Using neutron reflectivity, we have characterized the structure of mixed DPPE:GM(1) lipid monolayers before and during the binding of cholera toxin (CTAB(5)) or its B-subunit (CTB(5)). Structural parameters such as the density and thickness of the lipid layer, extension of the GM(1) oligosaccharide headgroup, and orientation and position of the protein upon binding are reported. The density of the lipid layer was found to decrease slightly upon protein binding. However, the A-subunit of the whole toxin is clearly located below the B-pentameric ring, away from the monolayer, and does not penetrate into the lipid layer before enzymatic cleavage. Using Monte Carlo simulations, the observed monolayer expansion was found to be consistent with geometrical constraints imposed on DPPE by multivalent binding of GM(1) by the toxin. Our findings suggest that the mechanism of membrane translocation by the protein may be aided by alterations in lipid packing.

Atmospheric Pressure Photoionization. 1. General Properties for LC/MS

In this work, we describe the performance of an atmospheric pressure photoionization (APPI) source for sampling liquid flows. The results presented here primarily focus on the mechanism of direct photoionization (PI), as compared to the dopant mechanism of PI. Measured detection limits for direct APPI were comparable to atmospheric pressure chemical ionization (APCI; e.g., 1 pg for reserpine). The ion signal is linear up to 10 ng injected quantity, with a useful dynamic range exceeding 100 ng. Evidence is presented indicating that APPI achieves significantly better sensitivity than APCI at flow rates below 200 microL/min, making it a useful source for capillary liquid chromatography and capillary electrophoresis. Results are presented indicating that APPI is less susceptible to ion suppression and salt buffer effects than APCI and electrospray ionization (ESI). The principal benefit of APPI, as compared to other ionization sources, is in efficiently ionizing broad classes of nonpolar compounds. Thus, APPI is an important complement to ESI and APCI by expanding the range and classes of compounds that can be analyzed. In this paper, we also discuss the role of direct APPI vs PI-induced APCI using dopants.

Pressure overload alters stress-strain properties of the developing chick heart

As a first step in investigating a control mechanism regulating stress and/or strain in the embryonic heart, this study tests the hypothesis that passive mechanical properties of left ventricular (LV) embryonic myocardium change with chronically increased pressure during the chamber septation period. Conotruncal banding (CTB) created ventricular pressure overload in chicks from Hamburger-Hamilton (HH) stage 21 (HH21) to HH27, HH29, or HH31. LV sections were cyclically stretched while biaxial strains and force were measured. Wall architecture was assessed with scanning electron microscopy. In controls, porosity-adjusted stress-strain relations decreased significantly from HH27 to HH31. CTB at HH21 resulted in significantly stiffer stress-strain relations by HH27, with larger increases at HH29 and HH31, and nearly constant wall thickness. Strain patterns, hysteresis, and loading-curve convergence showed few differences after CTB. Trabecular extent decreased with age, but neither extent nor porosity changed significantly after CTB. The stiffened stress-strain relations and constant wall thickness suggest that mechanical load may play a regulatory role in this response.

Mycobacterium bovis (bovine TB) exposure as a recreational risk for hunters: results of a Michigan Hunter Survey, 2001

SETTING

Tuberculosis caused by Mycobacterium bovis (bovine TB) is endemic in the white-tailed deer population of north-eastern Michigan. Hunters may be exposed to M. bovis via cutaneous inoculation while field dressing deer or by ingestion of undercooked venison. Michigan hunters have received inconsistent messages about their risk of acquiring tuberculosis from recreational exposure to deer. The most common health advice offered has been to wear gloves while field dressing deer and to cook venison products thoroughly.

OBJECTIVE

Data were collected to quantify these self-protective activities and to characterize hunters practicing these activities.

DESIGN

In 2001, we surveyed 1833 hunters who had successfully harvested deer in or near Michigan's bovine TB endemic area in 2000.

RESULTS

The survey response rate was 78%. Most hunters (89%) reported field dressing deer, 43% of whom wore gloves. Most hunters (95%) reported eating venison, 55% of whom reported their venison was always cooked thoroughly. Several hunter characteristics, including older age, female sex, higher awareness level, and area of residence, were significantly associated with the practice of these self-protective activities.

CONCLUSION

The survey results suggest that hunters should receive consistent advice encouraging glove use while field dressing deer and the thorough cooking of venison products before consumption.

Prenatal diagnosis of 21-hydroxylase deficiency caused by gene conversion and rearrangements: pitfalls and molecular diagnostic solutions

OBJECTIVES

The present paper reports the prenatal diagnosis of congenital adrenal hyperplasia (CAH) in two cases of 21-hydroxylase deficiency. DNA diagnostic errors can be caused by the presence of the highly homologous 21-hydroxylase pseudogene, CYP21P, adjacent to the functional gene, CYP21. The present paper details how complex gene conversions and rearrangements between the CYP21 and CYP21P pose unique complications for prenatal diagnosis.

METHODS

Analysis of eight common mutations in the 21-hydroxylase gene as well as deletion of the entire gene is accomplished using polymerase chin reaction (PCR) followed by amplified created restriction site (ACRS) or allele-specific oligohybridization (ASO) and Southern blot followed by hybridization to a CYP21-specific probe. Linkage analysis was performed using microsatellite markers flanking the CYP21 gene.

RESULTS

The direct mutation detection assay indicated a complicated gene conversion and rearrangement in the probands of both families. Interpretation of these rearrangements made it difficult to determine whether or not the fetuses would be affected with CAH. Linkage studies revealed that each fetus had inherited both parental disease chromosomes and was therefore predicted to be affected with CAH.

CONCLUSION

As observed in the two reported cases, direct DNA analysis may provide limited information due to gene conversion or rearrangement between the CYP21 and CYP21P genes. These cases suggest that direct mutation detection should be supported by linkage analysis, whenever possible, to provide more comprehensive information for the family.

Conformation of the O-specific polysaccharide of Shigella dysenteriae type 1: molecular modeling shows a helical structure with efficient exposure of the antigenic determinant alpha-L-Rhap-(1-->2)-alpha-D-Galp

The O-specific polysaccharide of Shigella dysenteriae type 1, which has the repeating tetrasaccharide unit -->3)-alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->2)-alpha-D-Galp-(1-->3)-alpha-D-GlcNAcp-(1--> (A-B-C-D), is a major virulence factor, and it is believed that antibodies against this polysaccharide confer protection to the host. The conformational properties of fragments of this O-antigen were explored using systematic search with a modified HSEA method (GLYCAN) and with molecular mechanics MM3(96). The results show that the alpha-D-Gal-(1-->3)-alpha-D-GlcNAc linkage adopts two favored conformations, phi/psi approximately equal to -40 degrees /-30 degrees (I) and approximately 15 degrees /30 degrees (II), whereas the other glycosidic linkages only have a single favored phi/psi conformational range. MM3 indicates that the trisaccharide B-C-D and tetrasaccharides containing the B-C-D moiety exist as two different conformers, distinguished by the conformations I and II of the C-D linkage. For the pentasaccharide A-B-C-D-A' and longer fragments, the calculations show preference for the C-D conformation II. These results can explain previously reported nuclear magnetic resonance data. The pentasaccharide in its favored conformation II is sharply bent, with the galactose residue exposed at the vertex. This hairpin conformation of the pentasaccharide was successfully docked with the binding site of a monoclonal IgM antibody (E3707 E9) that had been homology modeled from known crystal structures. For fragments made of repetitive tetrasaccharide units, the hairpin conformation leads to a left-handed helical structure with the galactose residues protruding radially at the helix surface. This arrangement results in a pronounced exposure of the galactose and also the adjacent rhamnose in each repeating unit, which is consistent with the known role of the as alpha-L-Rhap-(1-->2)-alpha-D-Galp moiety as a major antigenic epitope of this O-specific polysaccharide.

Methods of tissue extraction in advanced laparoscopy

Advances in laparoscopic surgery have revolved not only around new methods of tissue excision and repair, but also around specimen extraction. At the center of these recent advances is the need to be cost-effective and safe. Two particularly important advances in laparoscopic tissue extraction are use of electronic power morcellators, to cut up and remove large masses, and specimen bags to remove the extracted tissue safely. Although morcellators offer tremendous time savings, and can actually reduce the risk of hernia formation because fascia need not be torn or stretched, the use of power morcellators is not without concern. The sharp rotating blade can damage normal organs. Furthermore, one must watch closely so that morcellated specimens are not inadvertently misplaced. Specimen bags are also important, both in malignant and in benign conditions. Ultimately, the problem is spillage of tissue, whether it be cancer cells or products of conception. Although some specimen bags are equipped with self-opening devices, the largest bags must be opened manually.