Variant calling and benchmarking in an era of complete human genome sequences.

Genetic variant calling from DNA sequencing has enabled understanding of germline variation in hundreds of thousands of humans. Sequencing technologies and variant-calling methods have advanced rapidly, routinely providing reliable variant calls in most of the human genome. We describe how advances in long reads, deep learning, de novo assembly and pangenomes have expanded access to variant calls in increasingly challenging, repetitive genomic regions, including medically relevant regions, and how new benchmark sets and benchmarking methods illuminate their strengths and limitations. Finally, we explore the possible future of more complete characterization of human genome variation in light of the recent completion of a telomere-to-telomere human genome reference assembly and human pangenomes, and we consider the innovations needed to benchmark their newly accessible repetitive regions and complex variants.

Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes.

Advancements in sequencing technologies and assembly methods enable the regular production of high-quality genome assemblies characterizing complex regions. However, challenges remain in efficiently interpreting variation at various scales, from smaller tandem repeats to megabase rearrangements, across many human genomes. We present a PanGenome Research Tool Kit (PGR-TK) enabling analyses of complex pangenome structural and haplotype variation at multiple scales. We apply the graph decomposition methods in PGR-TK to the class II major histocompatibility complex demonstrating the importance of the human pangenome for analyzing complicated regions. Moreover, we investigate the Y-chromosome genes, DAZ1/DAZ2/DAZ3/DAZ4, of which structural variants have been linked to male infertility, and X-chromosome genes OPN1LW and OPN1MW linked to eye disorders. We further showcase PGR-TK across 395 complex repetitive medically important genes. This highlights the power of PGR-TK to resolve complex variation in regions of the genome that were previously too complex to analyze.

scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression.

SUMMARY: Single-cell Hi-C (scHi-C) protocol helps identify cell-type-specific chromatin interactions and sheds light on cell differentiation and disease progression. Despite providing crucial insights, scHi-C data is often underutilized due to the high cost and the complexity of the experimental protocol. We present a deep learning framework, scGrapHiC, that predicts pseudo-bulk scHi-C contact maps using pseudo-bulk scRNA-seq data. Specifically, scGrapHiC performs graph deconvolution to extract genome-wide single-cell interactions from a bulk Hi-C contact map using scRNA-seq as a guiding signal. Our evaluations show that scGrapHiC, trained on seven cell-type co-assay datasets, outperforms typical sequence encoder approaches. For example, scGrapHiC achieves a substantial improvement of 23.2% in recovering cell-type-specific Topologically Associating Domains over the baselines. It also generalizes to unseen embryo and brain tissue samples. scGrapHiC is a novel method to generate cell-type-specific scHi-C contact maps using widely available genomic signals that enables the study of cell-type-specific chromatin interactions. AVAILABILITY AND IMPLEMENTATION: The GitHub link: https://github.com/rsinghlab/scGrapHiC contains the source code of scGrapHiC and associated scripts to preprocess publicly available datasets to produce the results and visualizations we have discuss in this manuscript.

XRCC1 mutation is associated with PARP1 hyperactivation and cerebellar ataxia.

XRCC1 is a molecular scaffold protein that assembles multi-protein complexes involved in DNA single-strand break repair. Here we show that biallelic mutations in the human XRCC1 gene are associated with ocular motor apraxia, axonal neuropathy, and progressive cerebellar ataxia. Cells from a patient with mutations in XRCC1 exhibited not only reduced rates of single-strand break repair but also elevated levels of protein ADP-ribosylation. This latter phenotype is recapitulated in a related syndrome caused by mutations in the XRCC1 partner protein PNKP and implicates hyperactivation of poly(ADP-ribose) polymerase/s as a cause of cerebellar ataxia. Indeed, remarkably, genetic deletion of Parp1 rescued normal cerebellar ADP-ribose levels and reduced the loss of cerebellar neurons and ataxia in Xrcc1-defective mice, identifying a molecular mechanism by which endogenous single-strand breaks trigger neuropathology. Collectively, these data establish the importance of XRCC1 protein complexes for normal neurological function and identify PARP1 as a therapeutic target in DNA strand break repair-defective disease.

Quantum-cascade-laser-absorption-spectroscopy diagnostic for temperature, pressure, and NO X 2 Π 1/2 at 500 kHz in shock-heated air at elevated pressures.

The design, validation, and application of a quantum-cascade-laser-absorption-spectroscopy diagnostic for measuring gas temperature, pressure, and nitric oxide (NO) in high-temperature air are presented. A distributed-feedback quantum-cascade laser (QCL) centered near 1976c m -1 was used to scan across two transitions of NO in its ground electronic state (X 2 Π 1/2). A measurement rate of 500 kHz was achieved using a single QCL by: (1) performing current modulation through a bias-tee, and (2) targeting closely spaced transitions with a large difference in lower-state energy. The diagnostic was validated in a mixture of 95% argon and 5% NO, which was shock-heated to ≈2000 to 3700 K. The average mean percent differences between laser-absorption-spectroscopy (LAS) measurements and predictions from shock-jump relations for temperature, pressure, and NO mole fraction were 3.1%, 4.1%, and 6.5%, respectively. The diagnostic was then applied to characterize shock-heated air at high temperatures (up to ≈5500K) and high pressures (up to 12 atm) behind either incident or reflected shocks. The LAS measurements were compared to theoretical predictions from shock-jump relations, pressure sensors mounted in the wall of the shock tube, and equilibrium values of the NO mole fraction. The average mean percent differences between LAS measurements and their aforementioned reference values were 3.2%, 10.8%, and 10.4% for temperature, pressure, and NO mole fraction, respectively. Last, a comparison between a measured NO mole fraction time history and a time-stepped homogeneous reactor simulation performed using two different chemical kinetics mechanisms is presented.

Hypertension and Gastrointestinal Bleed in COVID-19 Patients: Associations with Mortality, Acute Kidney Injury, Vasopressor Use, and Mechanical Ventilation Use.

There are mixed findings on the association of hypertension or gastrointestinal bleed (GIB) with mortality in COVID-19 patients but no research on the combination of both hypertension and GIB with mortality in COVID-19 patients. We study in COVID-19 patients the association of hypertension and GIB with mortality, acute kidney injury (AKI), vasopressor use, and/or mechanical ventilation. This is a retrospective study of COVID-19 patients who were categorized into groups of no GIB/no hypertension (n = 653), yes hypertension/no GIB (n = 1,620), yes GIB/no hypertension (n = 104), or yes GIB/yes hypertension (n = 334). Covariates included demographics and medical history variables. In the multi-variate logistic regression analysis for the composite outcome of mortality, AKI, vasopressor use, and/or mechanical ventilation use, yes hypertension/no GIB (OR: 1.47, 95% CI: 1.13, 1.89, p <0.001) and yes GIB/no hypertension (OR: 1.68, 95% CI: 1.02, 2.78, p <0.001) were each significantly positively associated with the composite outcome. The yes GIB/yes hypertension group was not significantly associated with the composite outcome. In conclusion, we found that hypertension or GIB alone were each significantly associated with increased odds for the composite outcome while having both hypertension and GIB was protective and not significantly associated with the composite outcome. We recommend that clinicians be aware of such findings when treating patients with COVID-19, as those with both hypertension and GIB may not need as aggressive treatment as compared to those with either hypertension or GIB.

Unintended Perioperative Hypothermia and Surgical Site Infection in Children.

INTRODUCTION: Unintended perioperative hypothermia is associated with surgical site infection (SSI) in adults, prompting exhaustive efforts to maintain perioperative normothermia. Although these efforts are also made for pediatric patients, the association between hypothermia and SSI has not been demonstrated in children. We sought to determine whether perioperative hypothermia and other risk factors and clinical outcomes are associated with SSI in the pediatric population. MATERIALS AND METHODS: This case-control study took place from January 2014 through December 2016 and included patients at a National Surgical Quality Improvement Program-participant academic children's hospital. All surgical patients were included in this retrospective analysis. SSI rates were determined. A univariate analysis was performed to determine clinical factors associated with SSI. A multivariate regression analysis was then performed to determine the predictive effect of minimum perioperative temperature for SSI. RESULTS: This study included 3541 patients, of which 92 (2.6%) developed SSI. A univariate analysis showed associations among SSI and higher perioperative temperatures, surgical specialty of otolaryngology and general surgery, and wound classification (American Society of Anesthesiologists [ASA] classification III and IV). A multivariate analysis determined the odds of SSI increased by a factor of 1.6 for every 1°C increase in minimum perioperative temperature. CONCLUSIONS: Unintended perioperative hypothermia in our pediatric patients was inversely associated with SSI. This finding suggests that pediatric SSI prevention may not require the efforts made for adult patients to maintain normothermia.

Pulse-burst spontaneous Raman thermometry of unsteady wave phenomena in a shock tube.

A high-speed temperature diagnostic based on spontaneous Raman scattering (SRS) was demonstrated using a pulse-burst laser. The technique was first benchmarked in near-adiabatic ${{\rm H}_2} \text{-} {\rm air}$ flames at a data-acquisition rate of 5 kHz using an integrated pulse energy of 1.0 J per realization. Both the measurement precision and accuracy in the flame were within 3% of adiabatic predictions. This technique was then evaluated in a challenging free-piston shock tube environment operated at a shock Mach number of 3.5. SRS thermometry resolved the temperature in post-incident and post-reflected shock flows at a repetition rate of 3 kHz and clearly showed cooling associated with driver expansion waves. Collectively, this Letter represents a major advancement for SRS in impulsive facilities, which had previously been limited to steady state regions or single-shot acquisition.

Peanut Allergen Powder-dnfp: A Novel Oral Immunotherapy to Mitigate Peanut Allergy.

OBJECTIVE: To review data on efficacy and safety of peanut allergen powder-dnfp (PAP; Palforzia), a novel oral immunotherapy for peanut allergy, a common food allergy. DATA SOURCES: A PubMed/CINAHL search in English was performed from inception to June 30, 2020, using the search words peanut allergy, desensitization, ARA101, and peanut oral immunotherapy. STUDY SELECTION AND DATA EXTRACTION QUANTIFICATION: Published phase 2 and 3 clinical trials, documents presented to the Food and Drug Administration, and supplemental study documentation were reviewed. Articles evaluated PAP's pharmacology, pharmacokinetics, mechanism of action, efficacy, and safety. DATA SYNTHESIS: PAP was efficacious and safe for treatment of peanut allergy in mostly Caucasian children, 4 to 17 years old. A key phase III clinical trial showed a statistically significant difference (primary end point) between PAP 600 mg and placebo groups (67.2% vs 4%; P < 0.001). During initial dose escalation and updosing phases, gastrointestinal and respiratory tract allergic reactions (ARs) were more common in the PAP group. More epinephrine rescue was used in the PAP group. RELEVANCE TO PATIENT CARE AND CLINICAL PRACTICE: Oral immunotherapy for desensitization of peanut allergy was shown to reduce the severity of reactions if accidental allergen exposure occurs. Risk evaluation and mitigation strategy certification is required for pharmacies, health care providers, and clinics. More data in real-world populations will enhance its effectiveness. CONCLUSIONS: In patients 4 to 17 years old, PAP mitigated ARs, including anaphylaxis, that may occur with accidental peanut exposure. Although there are risks, it was efficacious in more than two-thirds of participants in phase 2 and phase 3 efficacy trials.

Nutraceuticals Synergistically Promote Osteogenesis in Cultured 7F2 Osteoblasts and Mitigate Inhibition of Differentiation and Maturation in Simulated Microgravity.

Microgravity is known to impact bone health, similar to mechanical unloading on Earth. In the absence of countermeasures, bone formation and mineral deposition are strongly inhibited in Space. There is an unmet need to identify nutritional countermeasures. Curcumin and carnosic acid are phytonutrients with anticancer, anti-inflammatory, and antioxidative effects and may exhibit osteogenic properties. Zinc is a trace element essential for bone formation. We hypothesized that these nutraceuticals could counteract the microgravity-induced inhibition of osteogenic differentiation and function. To test this hypothesis, we cultured 7F2 murine osteoblasts in simulated microgravity (SMG) in a Random Positioning Machine in the presence and absence of curcumin, carnosic acid, and zinc and evaluated cell proliferation, function, and differentiation. SMG enhanced cell proliferation in osteogenic medium. The nutraceuticals partially reversed the inhibitory effects of SMG on alkaline phosphatase (ALP) activity and did not alter the SMG-induced reduction in the expression of osteogenic marker genes in osteogenic medium, while they promoted osteoblast proliferation and ALP activity in the absence of traditional osteogenic media. We further observed a synergistic effect of the intermix of the phytonutrients on ALP activity. Intermixes of phytonutrients may serve as convenient and effective nutritional countermeasures against bone loss in space.

metagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data.

SUMMARY: We developed the metagenomeFeatures R Bioconductor package along with annotation packages for three 16S rRNA databases (Greengenes, RDP and SILVA) to facilitate working with 16S rRNA databases and marker-gene survey feature data. The metagenomeFeatures package defines two classes, MgDb for working with 16S rRNA sequence databases, and mgFeatures for marker-gene survey feature data. The associated annotation packages provide a consistent interface to the different databases facilitating database comparison and exploration. The mgFeatures-class represents a crucial step in the development of a common data structure for working with 16S marker-gene survey data in R. AVAILABILITY AND IMPLEMENTATION: https://bioconductor.org/packages/release/bioc/html/metagenomeFeatures.html. SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.

Metaviz: interactive statistical and visual analysis of metagenomic data.

Large studies profiling microbial communities and their association with healthy or disease phenotypes are now commonplace. Processed data from many of these studies are publicly available but significant effort is required for users to effectively organize, explore and integrate it, limiting the utility of these rich data resources. Effective integrative and interactive visual and statistical tools to analyze many metagenomic samples can greatly increase the value of these data for researchers. We present Metaviz, a tool for interactive exploratory data analysis of annotated microbiome taxonomic community profiles derived from marker gene or whole metagenome shotgun sequencing. Metaviz is uniquely designed to address the challenge of browsing the hierarchical structure of metagenomic data features while rendering visualizations of data values that are dynamically updated in response to user navigation. We use Metaviz to provide the UMD Metagenome Browser web service, allowing users to browse and explore data for more than 7000 microbiomes from published studies. Users can also deploy Metaviz as a web service, or use it to analyze data through the metavizr package to interoperate with state-of-the-art analysis tools available through Bioconductor. Metaviz is free and open source with the code, documentation and tutorials publicly accessible.

Compound heterozygous mutations in the gene PIGP are associated with early infantile epileptic encephalopathy.

There are over 150 known human proteins which are tethered to the cell surface via glycosylphosphatidylinositol (GPI) anchors. These proteins play a variety of important roles in development, and particularly in neurogenesis. Not surprisingly, mutations in the GPI anchor biosynthesis and remodeling pathway cause a number of developmental disorders. This group of conditions has been termed inherited GPI deficiencies (IGDs), a subgroup of congenital disorders of glycosylation; they present with variable phenotypes, often including seizures, hypotonia and intellectual disability. Here, we report two siblings with compound heterozygous variants in the gene phosphatidylinositol glycan anchor biosynthesis, class P (PIGP) (NM_153681.2: c.74T > C;p.Met25Thr and c.456delA;p.Glu153AsnFs*34). PIGP encodes a subunit of the enzyme that catalyzes the first step of GPI anchor biosynthesis. Both children presented with early-onset refractory seizures, hypotonia, and profound global developmental delay, reminiscent of other IGD phenotypes. Functional studies with patient cells showed reduced PIGP mRNA levels, and an associated reduction of GPI-anchored cell surface proteins, which was rescued by exogenous expression of wild-type PIGP. This work associates mutations in the PIGP gene with a novel autosomal recessive IGD, and expands our knowledge of the role of PIG genes in human development.

Whole-transcriptome sequencing in blood provides a diagnosis of spinal muscular atrophy with progressive myoclonic epilepsy.

At least 15% of the disease-causing mutations affect mRNA splicing. Many splicing mutations are missed in a clinical setting due to limitations of in silico prediction algorithms or their location in noncoding regions. Whole-transcriptome sequencing is a promising new tool to identify these mutations; however, it will be a challenge to obtain disease-relevant tissue for RNA. Here, we describe an individual with a sporadic atypical spinal muscular atrophy, in whom clinical DNA sequencing reported one pathogenic ASAH1 mutation (c.458A>G;p.Tyr153Cys). Transcriptome sequencing on patient leukocytes identified a highly significant and atypical ASAH1 isoform not explained by c.458A>G(p<10-16 ). Subsequent Sanger-sequencing identified the splice mutation responsible for the isoform (c.504A>C;p.Lys168Asn) and provided a molecular diagnosis of autosomal-recessive spinal muscular atrophy with progressive myoclonic epilepsy. Our findings demonstrate the utility of RNA sequencing from blood to identify splice-impacting disease mutations for nonhematological conditions, providing a diagnosis for these otherwise unsolved patients.

Homozygous mutations in MFN2 cause multiple symmetric lipomatosis associated with neuropathy.

Multiple symmetric lipomatosis (MSL) is a mitochondrial disorder with impaired brown fat metabolism that has been associated with MERRF mutations in some, but not all, patients. We studied a sibling pair and an unrelated indiviadual who presented with MSL and neuropathy to determine the genetic etiology of this disorder in patients who did not carry the MSL-associated MERRF mutation. Whole-exome sequencing was performed on the siblings, and a rare, shared homozygous mutation in MFN2 (c.2119C>T: p.R707W) was identified. The mutation was not present in their healthy siblings. In silico programs predict it to be pathogenic, and heterozygous carriers of the MFN2 p.R707W substitution are known to have Charcot-Marie-Tooth (CMT) disease. A third, unrelated patient with multiple symmetrical lipomatosis and neuropathy also harbored the same homozygous mutation and had been previously diagnosed with CMT. Functional studies in patient fibroblasts demonstrate that the p.R707W substitution impairs homotypic (MFN2-MFN2) protein interactions required for normal activity and renders mitochondria prone to perinuclear aggregation. These findings show that homozygous mutations at p.R707W in MFN2 are a novel cause of multiple symmetrical lipomatosis.

Privacy-preserving microbiome analysis using secure computation.

MOTIVATION: Developing targeted therapeutics and identifying biomarkers relies on large amounts of research participant data. Beyond human DNA, scientists now investigate the DNA of micro-organisms inhabiting the human body. Recent work shows that an individual's collection of microbial DNA consistently identifies that person and could be used to link a real-world identity to a sensitive attribute in a research dataset. Unfortunately, the current suite of DNA-specific privacy-preserving analysis tools does not meet the requirements for microbiome sequencing studies. RESULTS: To address privacy concerns around microbiome sequencing, we implement metagenomic analyses using secure computation. Our implementation allows comparative analysis over combined data without revealing the feature counts for any individual sample. We focus on three analyses and perform an evaluation on datasets currently used by the microbiome research community. We use our implementation to simulate sharing data between four policy-domains. Additionally, we describe an application of our implementation for patients to combine data that allows drug developers to query against and compensate patients for the analysis. AVAILABILITY AND IMPLEMENTATION: The software is freely available for download at: http://cbcb.umd.edu/∼hcorrada/projects/secureseq.html SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: hcorrada@umiacs.umd.edu.

Web-Based Video Assessments of Operative Performance for Remote Telementoring.

INTRODUCTION: Performance-based feedback is critical to surgical skills acquisition. Barriers of geography and time limit trainees' access to expert mentorship. In this study, we hypothesized that telementoring using an asynchronous, web-based video interface would allow trainees to receive systematic feedback from expert mentors despite these barriers. MATERIALS AND METHODS: Between October 2014 and October 2016, 18 surgeons in Brazil, Dominican Republic, Haiti, and Paraguay underwent in-person training in Lichtenstein for hernioplasty or laparoscopic total extraperitoneal inguinal hernia repair. After initial training, surgeons submitted 6- to 12-month interval operative videos for expert review. Expert surgeons reviewed each video using the Surgus web platform with performance metrics adapted from the Operative Performance Rating Scale (OPRS). The time required to perform video review, number of freeform comments, mean OPRS scores, and variance of OPRS scores among telementors was assessed. RESULTS: A total of 18 surgeons submitted 20 operative videos, and three expert surgeons reviewed each video using the Surgus platform. The median time to perform video review was 20 minutes. Median number of freeform verbal comments was eight. Mean OPRS overall performance scores were 3.9 ± 0.9 (scale of five). Mean variance in scoring among telementors for overall performance was 0.25 (maximum 5.29), suggesting a high degree of concordance. CONCLUSIONS: Video-based assessments had a high degree of concordance among expert raters. Asynchronous performance reviews by telementors offer opportunities for longitudinal feedback that overcome geographical, material, and temporal disparities. This platform offers a means of sharing expertise in surgical training, continuing education, credentialing, and global health.

Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature.

BACKGROUND: Chromosomal deletions encompassing DYRK1A have been associated with intellectual disability for several years. More recently, point mutations in DYRK1A have been shown to be responsible for a recognizable syndrome characterized by microcephaly, developmental delay and intellectual disability (ID) as well as characteristic facial features. Here we present 2 individuals with novel mutations in DYRK1A, and a review of the cases reported to date. CASE PRESENTATION: Both individuals presented with the well-known characteristic features, as well as rarer anomalies seen in a minority of patients. Patient 1 presented shortly after birth with an enlarged cisterna magna, distal contractures, and distinctive facies that included bitemporal narrowing and deep set eyes. A de novo splice site mutation in DYRK1A [c.951 + 4_951 + 7delAGTA; p.Val222Aspfs*22] was identified by next generation sequencing. Patient 2 presented at 7 months of age with microcephaly and dysmorphic features. She went several years without a diagnosis until a de novo DYRK1A nonsense mutation [c.787C>T; p.(Arg263*)] was identified at age 12. These individuals, and the 52 cases reviewed from the literature, show the characteristic features of the DYRK1A-related syndrome including global developmental delay, ID, microcephaly, feeding difficulties, and the facial gestalt. Other common findings include seizures, vision defects, brain abnormalities and skeletal abnormalities of the hands and feet. Less common features include optic nerve defects, contractures, ataxia, and cardiac anomalies. CONCLUSION: DYRK1A testing should be considered in individuals with the facial features, intellectual disability and post-natal microcephaly. Once diagnosed with DYRK1A-related intellectual disability, a cardiac and ophthalmologic assessment would be recommended as would routine surveillance by a pediatrician for psychomotor development, growth, and feeding.

Mouse model of endoscopically ablated enteric nervous system.

BACKGROUND: Current transgenic animal models of Hirschsprung disease are restricted by limited survival and need for special dietary care. We used small animal colonoscopy to produce chemically ablated enteric nervous system in the distal colon and rectum of normal mice. MATERIALS AND METHODS: Adult C57BL/6 mice underwent colonoscopy with submucosal injection of 75-100 µL of saline (n = 2) or 0.002% (n = 2), 0.02% (n = 15), or 0.2% (n = 2) benzalkonium chloride (BAC). Each mouse received 1-3 injections in the distal colon and rectum. Mice were sacrificed on postprocedure day 7 or 28. Injection sites were analyzed histologically and with immunostaining for ß-tubulin III. RESULTS: Submucosal injection of 0.02% BAC resulted in megacolon and obliteration of 82 ± 8.8% of myenteric ganglia at the injection site on postprocedure day 7 compared with normal colon. This effect was sustained until day 28. Injection of 0.002% BAC had little effect on the myenteric neuronal network at these time points. Multiple injections of 0.002% or 0.02% BAC (up to three injections per mouse) were well tolerated. Injection of 0.2% BAC caused acute toxicity or death. CONCLUSIONS: A novel model of chemically ablated enteric nervous system in the mouse colon and rectum is introduced. This model can be valuable in evaluating targeted cell delivery therapies for Hirschsprung disease.

De novo mutations in the motor domain of KIF1A cause cognitive impairment, spastic paraparesis, axonal neuropathy, and cerebellar atrophy.

KIF1A is a neuron-specific motor protein that plays important roles in cargo transport along neurites. Recessive mutations in KIF1A were previously described in families with spastic paraparesis or sensory and autonomic neuropathy type-2. Here, we report 11 heterozygous de novo missense mutations (p.S58L, p.T99M, p.G102D, p.V144F, p.R167C, p.A202P, p.S215R, p.R216P, p.L249Q, p.E253K, and p.R316W) in KIF1A in 14 individuals, including two monozygotic twins. Two mutations (p.T99M and p.E253K) were recurrent, each being found in unrelated cases. All these de novo mutations are located in the motor domain (MD) of KIF1A. Structural modeling revealed that they alter conserved residues that are critical for the structure and function of the MD. Transfection studies suggested that at least five of these mutations affect the transport of the MD along axons. Individuals with de novo mutations in KIF1A display a phenotype characterized by cognitive impairment and variable presence of cerebellar atrophy, spastic paraparesis, optic nerve atrophy, peripheral neuropathy, and epilepsy. Our findings thus indicate that de novo missense mutations in the MD of KIF1A cause a phenotype that overlaps with, while being more severe, than that associated with recessive mutations in the same gene.