Combined Bioinformatic and Splicing Analysis of Likely Benign Intronic and Synonymous Variants Reveals Evidence for Pathogenicity.

Background: Current clinical variant analysis pipelines focus on coding variants and intronic variants within 10-20 bases of an exon-intron boundary that may affect splicing. The impact of newer splicing prediction algorithms combined with in vitro splicing assays on rare variants currently considered Benign/Likely Benign (B/LB) is unknown. Methods: Exome sequencing data from 576 pediatric cancer patients enrolled in the Texas KidsCanSeq study were filtered for intronic or synonymous variants absent from population databases, predicted to alter splicing via SpliceAI (>0.20), and scored as potentially deleterious by CADD (>10.0). Total cellular RNA was extracted from monocytes and RT-PCR products analyzed. Subsequently, rare synonymous or intronic B/LB variants in a subset of genes submitted to ClinVar were similarly evaluated. Variants predicted to lead to a frameshifted splicing product were functionally assessed using an in vitro splicing reporter assay in HEK-293T cells. Results: KidsCanSeq exome data analysis revealed a rare, heterozygous, intronic variant (NM_177438.3(DICER1):c.574-26A>G) predicted by SpliceAI to result in gain of a secondary splice acceptor site. The proband had a personal and family history of pleuropulmonary blastoma consistent with DICER1 syndrome but negative clinical sequencing reports. Proband RNA analysis revealed alternative DICER1 transcripts including the SpliceAI-predicted transcript.Similar bioinformatic analysis of synonymous or intronic B/LB variants (n=31,715) in ClinVar from 61 Mendelian disease genes yielded 18 variants, none of which could be scored by MaxEntScan. Eight of these variants were assessed (DICER1 n=4, CDH1 n=2, PALB2 n=2) using in vitro splice reporter assay and demonstrated abnormal splice products (mean 66%; range 6% to 100%). Available phenotypic information from submitting laboratories demonstrated DICER1 phenotypes in 2 families (1 variant) and breast cancer phenotypes for PALB2 in 3 families (2 variants). Conclusions: Our results demonstrate the power of newer predictive splicing algorithms to highlight rare variants previously considered B/LB in patients with features of hereditary conditions. Incorporation of SpliceAI annotation of existing variant data combined with either direct RNA analysis or in vitro assays has the potential to identify disease-associated variants in patients without a molecular diagnosis.

Allele biased transcription factor binding across human brain regions gives mechanistic insight into eQTLs.

Transcription Factors (TFs) influence gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Because genomic localization of TFs is in part driven by TF recognition of DNA sequence, variation in TF binding sites can disrupt TF-DNA associations and affect gene regulation. To identify variants that impact TF binding in human brain tissues, we quantified allele bias for 93 TFs analyzed with ChIP-seq experiments of multiple structural brain regions from two donors. Using graph genomes constructed from phased genomic sequence data, we compared ChIP-seq signal between alleles at heterozygous variants within each tissue sample from each donor. Comparison of results from different brain regions within donors and the same regions between donors provided measures of allele bias reproducibility. We identified thousands of DNA variants that show reproducible bias in ChIP-seq for at least one TF. We found that alleles that are rarer in the general population were more likely than common alleles to exhibit large biases, and more frequently led to reduced TF binding. Combining ChIP-seq with RNA-seq, we identified TF-allele interaction biases with RNA bias in a phased allele linked to 6,709 eQTL variants identified in GTEx data, 3,309 of which were found in neural contexts. Our results provide insights into the effects of both common and rare variation on gene regulation in the brain. These findings can facilitate mechanistic understanding of cis-regulatory variation associated with biological traits, including disease.

Parents' Perspectives on the Utility of Genomic Sequencing in the Neonatal Intensive Care Unit.

BACKGROUND: It is critical to understand the wide-ranging clinical and non-clinical effects of genome sequencing (GS) for parents in the NICU context. We assessed parents' experiences with GS as a first-line diagnostic tool for infants with suspected genetic conditions in the NICU. METHODS: Parents of newborns (N = 62) suspected of having a genetic condition were recruited across five hospitals in the southeast United States as part of the SouthSeq study. Semi-structured interviews (N = 78) were conducted after parents received their child's sequencing result (positive, negative, or variants of unknown significance). Thematic analysis was performed on all interviews. RESULTS: Key themes included that (1) GS in infancy is important for reproductive decision making, preparing for the child's future care, ending the diagnostic odyssey, and sharing results with care providers; (2) the timing of disclosure was acceptable for most parents, although many reported the NICU environment was overwhelming; and (3) parents deny that receiving GS results during infancy exacerbated parent-infant bonding, and reported variable impact on their feelings of guilt. CONCLUSION: Parents reported that GS during the neonatal period was useful because it provided a "backbone" for their child's care. Parents did not consistently endorse negative impacts like interference with parent-infant bonding.

Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing.

PURPOSE: Neurodevelopmental disorders (NDDs) often result from rare genetic variation, but genomic testing yield for NDDs remains below 50%, suggesting that clinically relevant variants may be missed by standard analyses. Here, we analyze "poison exons" (PEs), which are evolutionarily conserved alternative exons often absent from standard gene annotations. Variants that alter PE inclusion can lead to loss of function and may be highly penetrant contributors to disease. METHODS: We curated published RNA sequencing data from developing mouse cortex to define 1937 conserved PE regions potentially relevant to NDDs, and we analyzed variants found by genome sequencing in multiple NDD cohorts. RESULTS: Across 2999 probands, we found 6 novel clinically relevant variants in PE regions. Five of these variants are in genes that are part of the sodium voltage-gated channel alpha subunit family (SCN1A, SCN2A, and SCN8A), which is associated with epilepsies. One variant is in SNRPB, associated with cerebrocostomandibular syndrome. These variants have moderate to high computational impact assessments, are absent from population variant databases, and in genes with gene-phenotype associations consistent with each probands reported features. CONCLUSION: With a very minimal increase in variant analysis burden (average of 0.77 variants per proband), annotation of PEs can improve diagnostic yield for NDDs and likely other congenital conditions.

Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing.

Purpose: Neurodevelopmental disorders (NDDs) often result from rare genetic variation, but genomic testing yield for NDDs remains around 50%, suggesting some clinically relevant rare variants may be missed by standard analyses. Here we analyze "poison exons" (PEs) which, while often absent from standard gene annotations, are alternative exons whose inclusion results in a premature termination codon. Variants that alter PE inclusion can lead to loss-of-function and may be highly penetrant contributors to disease. Methods: We curated published RNA-seq data from developing mouse cortex to define 1,937 PE regions conserved between humans and mice and potentially relevant to NDDs. We then analyzed variants found by genome sequencing in multiple NDD cohorts. Results: Across 2,999 probands, we found six clinically relevant variants in PE regions that were previously overlooked. Five of these variants are in genes that are part of the sodium voltage-gated channel alpha subunit family ( SCN1A, SCN2A , and SCN8A ), associated with epilepsies. One variant is in SNRPB , associated with Cerebrocostomandibular Syndrome. These variants have moderate to high computational impact assessments, are absent from population variant databases, and were observed in probands with features consistent with those reported for the associated gene. Conclusion: With only a minimal increase in variant analysis burden (most probands had zero or one candidate PE variants in a known NDD gene, with an average of 0.77 per proband), annotation of PEs can improve diagnostic yield for NDDs and likely other congenital conditions.

Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype.

Neurodevelopmental disorders (NDDs) result from highly penetrant variation in hundreds of different genes, some of which have not yet been identified. Using the MatchMaker Exchange, we assembled a cohort of 27 individuals with rare, protein-altering variation in the transcriptional coregulator ZMYM3, located on the X chromosome. Most (n = 24) individuals were males, 17 of which have a maternally inherited variant; six individuals (4 male, 2 female) harbor de novo variants. Overlapping features included developmental delay, intellectual disability, behavioral abnormalities, and a specific facial gestalt in a subset of males. Variants in almost all individuals (n = 26) are missense, including six that recurrently affect two residues. Four unrelated probands were identified with inherited variation affecting Arg441, a site at which variation has been previously seen in NDD-affected siblings, and two individuals have de novo variation resulting in p.Arg1294Cys (c.3880C>T). All variants affect evolutionarily conserved sites, and most are predicted to damage protein structure or function. ZMYM3 is relatively intolerant to variation in the general population, is widely expressed across human tissues, and encodes a component of the KDM1A-RCOR1 chromatin-modifying complex. ChIP-seq experiments on one variant, p.Arg1274Trp, indicate dramatically reduced genomic occupancy, supporting a hypomorphic effect. While we are unable to perform statistical evaluations to definitively support a causative role for variation in ZMYM3, the totality of the evidence, including 27 affected individuals, recurrent variation at two codons, overlapping phenotypic features, protein-modeling data, evolutionary constraint, and experimentally confirmed functional effects strongly support ZMYM3 as an NDD-associated gene.

Genome sequencing as a first-line diagnostic test for hospitalized infants.

PURPOSE: SouthSeq is a translational research study that undertook genome sequencing (GS) for infants with symptoms suggestive of a genetic disorder. Recruitment targeted racial/ethnic minorities and rural, medically underserved areas in the Southeastern United States, which are historically underrepresented in genomic medicine research. METHODS: GS and analysis were performed for 367 infants to detect disease-causal variation concurrent with standard of care evaluation and testing. RESULTS: Definitive diagnostic (DD) or likely diagnostic (LD) genetic findings were identified in 30% of infants, and 14% of infants harbored an uncertain result. Only 43% of DD/LD findings were identified via concurrent clinical genetic testing, suggesting that GS testing is better for obtaining early genetic diagnosis. We also identified phenotypes that correlate with the likelihood of receiving a DD/LD finding, such as craniofacial, ophthalmologic, auditory, skin, and hair abnormalities. We did not observe any differences in diagnostic rates between racial/ethnic groups. CONCLUSION: We describe one of the largest-to-date GS cohorts of ill infants, enriched for African American and rural patients. Our results show the utility of GS because it provides early-in-life detection of clinically relevant genetic variations not detected by current clinical genetic testing, particularly for infants exhibiting certain phenotypic features.

Aberrant regulation of a poison exon caused by a non-coding variant in a mouse model of Scn1a-associated epileptic encephalopathy.

Dravet syndrome (DS) is a developmental and epileptic encephalopathy that results from mutations in the Nav1.1 sodium channel encoded by SCN1A. Most known DS-causing mutations are in coding regions of SCN1A, but we recently identified several disease-associated SCN1A mutations in intron 20 that are within or near to a cryptic and evolutionarily conserved "poison" exon, 20N, whose inclusion is predicted to lead to transcript degradation. However, it is not clear how these intron 20 variants alter SCN1A expression or DS pathophysiology in an organismal context, nor is it clear how exon 20N is regulated in a tissue-specific and developmental context. We address those questions here by generating an animal model of our index case, NM_006920.4(SCN1A):c.3969+2451G>C, using gene editing to create the orthologous mutation in laboratory mice. Scn1a heterozygous knock-in (+/KI) mice exhibited an ~50% reduction in brain Scn1a mRNA and Nav1.1 protein levels, together with characteristics observed in other DS mouse models, including premature mortality, seizures, and hyperactivity. In brain tissue from adult Scn1a +/+ animals, quantitative RT-PCR assays indicated that ~1% of Scn1a mRNA included exon 20N, while brain tissue from Scn1a +/KI mice exhibited an ~5-fold increase in the extent of exon 20N inclusion. We investigated the extent of exon 20N inclusion in brain during normal fetal development in RNA-seq data and discovered that levels of inclusion were ~70% at E14.5, declining progressively to ~10% postnatally. A similar pattern exists for the homologous sodium channel Nav1.6, encoded by Scn8a. For both genes, there is an inverse relationship between the level of functional transcript and the extent of poison exon inclusion. Taken together, our findings suggest that poison exon usage by Scn1a and Scn8a is a strategy to regulate channel expression during normal brain development, and that mutations recapitulating a fetal-like pattern of splicing cause reduced channel expression and epileptic encephalopathy.

Accuracy of whole-body HDP SPECT/CT, FDG PET/CT, and their combination for detecting bone metastases in breast cancer: an intra-personal comparison.

New generation SPECT/CT scanners allow rapid whole-body imaging, and potentially facilitate significantly improved diagnostic accuracy. Thus, the aim of this study was to compare the diagnostic accuracy of whole-body Tc-99m-HDP SPECT/CT, F-18-FDG PET/CT, and their combination for detecting bone metastases in breast cancer. Women with biopsy-proven breast cancer that were referred for whole-body SPECT/CT and FDG PET/CT were consecutively included in this retrospective study. Two blinded readers independently interpreted all scans. In a per-patient analysis, the diagnostic performances of whole-body SPECT/CT, FDG PET/CT, and their combination were compared using receiver operating characteristic (ROC) analysis. In a per-lesion analysis, the performances were compared using figures of merit (FoM) differences in Jackknife alternative free-response ROC analysis, which considers the location information. Follow-up served as reference standard. Overall, 25 consecutive women (median age: 55; range 38-82) with 117 lesions were included. The median follow-up was 21 months (2-46 months). The per-patient analysis revealed no significant differences in diagnostic performance (P = 0.16), while the per-lesion analysis revealed a diagnostic superiority of whole-body SPECT/CT over FDG PET/CT (P = 0.004). Specifically, the PET/CT FoM was significantly lower than the SPECT/CT FoM (FoM difference = -0.11, 95% CI [-0.21; -0.02], P = 0.021). No significant difference was observed between SPECT/CT and the combination of SPECT/CT and PET/CT. The per-lesion analysis suggest that SPECT/CT has a higher diagnostic accuracy than FDG PET/CT for the detection of bone metastases. Thus, SPECT/CT may be a useful adjunct to FDG PET/CT for staging of breast cancer patients.

Newly Diagnosed Breast Cancer: Comparison of Contrast-enhanced Spectral Mammography and Breast MR Imaging in the Evaluation of Extent of Disease.

Purpose To compare the diagnostic performances of contrast material-enhanced spectral mammography and breast magnetic resonance (MR) imaging in the detection of index and secondary cancers in women with newly diagnosed breast cancer by using histologic or imaging follow-up as the standard of reference. Materials and Methods This institutional review board-approved, HIPAA-compliant, retrospective study included 52 women who underwent breast MR imaging and contrast-enhanced spectral mammography for newly diagnosed unilateral breast cancer between March 2014 and October 2015. Of those 52 patients, 46 were referred for contrast-enhanced spectral mammography and targeted ultrasonography because they had additional suspicious lesions at MR imaging. In six of the 52 patients, breast cancer had been diagnosed at an outside institution. These patients were referred for contrast-enhanced spectral mammography and targeted US as part of diagnostic imaging. Images from contrast-enhanced spectral mammography were analyzed by two fellowship-trained breast imagers with 2.5 years of experience with contrast-enhanced spectral mammography. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value were calculated for both imaging modalities and compared by using the Bennett statistic. Results Fifty-two women with 120 breast lesions were included for analysis (mean age, 50 years; range, 29-73 years). Contrast-enhanced spectral mammography had similar sensitivity to MR imaging (94% [66 of 70 lesions] vs 99% [69 of 70 lesions]), a significantly higher PPV than MR imaging (93% [66 of 71 lesions] vs 60% [69 of 115 lesions]), and fewer false-positive findings than MR imaging (five vs 45) (P < .001 for all results). In addition, contrast-enhanced spectral mammography depicted 11 of the 11 secondary cancers (100%) and MR imaging depicted 10 (91%). Conclusion Contrast-enhanced spectral mammography is potentially as sensitive as MR imaging in the evaluation of extent of disease in newly diagnosed breast cancer, with a higher PPV. © RSNA, 2017.

In-bore magnetic resonance-guided transrectal biopsy for the detection of clinically significant prostate cancer.

PURPOSE: To determine the safety and efficacy of in-bore magnetic resonance-guided prostate biopsy (MRGB) for detection of clinically significant disease (CSD) in untreated men with known or suspected prostate cancer (PCa). METHODS: 512 patients underwent multiparametric magnetic resonance imaging (Mp-MRI) followed by MRGB at one of three centers in this IRB-approved, HIPAA-compliant, retrospective study. Exclusion criteria were prior prostate cancer therapy and incomplete Mp-MRI (n = 51). Patients (n = 461) were analyzed in two subcohorts: no prior PCa (NP) (n = 381) and active surveillance (AS) (n = 80). Detection rates of PCa and CSD (Gleason Score ≥3 + 4) were calculated and compared among subcohorts and by Mp-MRI assessment grade. Logistic regression was performed to identify predictors for detection of PCa and CSD. RESULTS: Mean patient age was 66 years, median prostate-specific antigen (PSA) was 7.5 ng/mL, and median prostate volume was 54 cc. A mean of 1.7 targets was sampled per gland. Significant adverse events (urosepsis and hematuria with obstruction) occurred in 1% (5/461). Overall PCa detection rates were 51% per patient (233/461) and 37% per lesion (282/757). 65% (151/233) of men with detected PCa had CSD. Per-patient PCa detection rates in the NP and AS subcohorts were 47% (178/381) and 69% (55/80), respectively, significantly higher in the AS group (p < 0.001). CSD was detected in 10% (47/451), 43% (96/225) and 84% (68/81) of lesions with Mp-MRI assessment grades of 3, 4, and 5, respectively. Older age, higher PSA, and lower prostate volume predicted MRGB detection of CSD (OR 1.07 and p = 0.003, OR 1.1 and p = 0.014, and OR 0.98 and p = 0.032, respectively). CONCLUSIONS: In-bore MRGB is safe and high yield for detection of CSD.

Use of MDCT to Differentiate Autoimmune Pancreatitis From Ductal Adenocarcinoma and Interstitial Pancreatitis.

OBJECTIVE: The purposes of this study were to identify the most common imaging features of autoimmune pancreatitis and to evaluate the utility of MDCT for differentiating autoimmune pancreatitis from two more frequently encountered differential diagnoses--pancreatic ductal adenocarcinoma and acute interstitial pancreatitis. MATERIALS AND METHODS: Dual-phase contrast-enhanced MDCT images of 91 patients (39 with autoimmune pancreatitis, 25 with pancreatic ductal adenocarcinoma, 27 with acute interstitial pancreatitis) were evaluated by two radiologists in consensus for distribution of pancreatic abnormality, sausage shape, low-attenuation halo, pancreatic duct dilatation, peripancreatic stranding, lymphadenopathy, biliary abnormality, vascular involvement, and renal lesions. Chi-square tests, multiple logistic regression analysis, and ROC analysis were performed. RESULTS: The most common imaging features of autoimmune pancreatitis were sausage shape (25/39 [64%]) and low-attenuation halo (23/39 [59%]). Pancreatic duct dilatation (20/25 [80%]) and biliary dilatation (11/25 [44%]) were most frequent in pancreatic ductal adenocarcinoma. Peripancreatic stranding (22/27 [81%]) was most frequent in acute interstitial pancreatitis. Sausage shape, low-attenuation halo, and absence of a pancreatic duct or biliary dilatation differentiated autoimmune pancreatitis from pancreatic ductal adenocarcinoma with an accuracy of 0.88. Sausage shape and absence of peripancreatic stranding differentiated autoimmune pancreatitis from acute interstitial pancreatitis with an accuracy of 0.82. There was no significant difference in the frequency of vascular involvement or of lymphadenopathy among these diagnoses. CONCLUSION: Typical cases of autoimmune pancreatitis can be accurately differentiated from pancreatic ductal adenocarcinoma and acute interstitial pancreatitis on the basis of characteristic MDCT features. However, autoimmune pancreatitis should be considered in the presence of atypical features.

Intraductal Cooling via a Nasobiliary Tube During Radiofrequency Ablation of Central Liver Tumors Reduces Biliary Injuries.

OBJECTIVE: The objective of our study was to determine the safety and efficacy of intraductal perfusion of chilled 5% dextrose in water (D5W) via an endoscopic nasobiliary tube (NBT) for the prevention of thermal bile duct injury in patients undergoing percutaneous radiofrequency ablation (RFA) of central liver tumors. MATERIALS AND METHODS: We performed a retrospective study comparing outcomes of 32 consecutive patients who underwent percutaneous RFA of central liver tumors without intraductal perfusion of chilled D5W (control cohort) and 14 consecutive patients who underwent temporary intraductal perfusion of chilled D5W at 2 mL/s via endoscopic NBT placement before RFA (endoscopic NBT cohort). The primary and secondary outcomes were the rate of biliary complications and local tumor progression, respectively. RESULTS: All patients tolerated the procedures well. There was a significantly lower rate of biliary complications in the endoscopic NBT cohort (0/14 patients, 0%) than in the control cohort (10/32 patients, 31%) (p < 0.03) with a trend toward improved preservation of liver function in the endoscopic NBT cohort (12/14 patients, 86%) compared with the control cohort (20/32 patients, 62%) (p = 0.05). There was no difference in the rate of local tumor progression between the endoscopic NBT cohort (4/19 tumors, 21%) and the control cohort (9/39 tumors, 23%) (p = 1.0). CONCLUSION: Perfusion of chilled water through an endoscopic NBT helps prevent thermal biliary injury during RFA of central liver tumors without increasing rates of local tumor progression.

Qualitative and quantitative MDCT features for differentiating clear cell renal cell carcinoma from other solid renal cortical masses.

OBJECTIVE: The purpose of this study was to differentiate clear cell renal cell carcinoma (RCC) from other solid renal masses on four-phase MDCT. MATERIALS AND METHODS: Our study cohort included all pathologically proven solid renal masses that underwent pretreatment four-phase MDCT at our institution from 2001 to 2012. Both retrospective qualitative analysis (blinded dual-radiologist evaluation of morphologic features: enhancement pattern, lesion contour, neovascularity, and calcification) and quantitative analysis (mean absolute and relative attenuation and changes in attenuation across phases) were performed. ANOVA with post-hoc analysis, Pearson chi-square tests, and ROC analysis were used. RESULTS: One hundred fifty-six consecutive patients (99 men, 57 women) with a mean age of 62.7 years (range, 26-91 years) had 165 solid renal masses (median size, 3.0 cm): 86 clear cell RCCs, 36 papillary RCCs, 10 chromophobe RCCs, 23 oncocytomas, and 10 lipid-poor angiomyolipomas. Kappa for interradiologist agreement regarding morphologic features was 0.33-0.76. There were significant associations between histologic subtype and enhancement pattern (p < 0.001), lesion contour (p < 0.014), and neovascularity (p < 0.001). Clear cell RCC had the highest mean relative corticomedullary attenuation (p < 0.02). Clear cell RCC had greater deenhancement than oncocytoma (p < 0.001); deenhancement less than 50 HU or relative corticomedullary attenuation greater than 0% differentiated clear cell RCC from oncocytoma with a positive predictive value of 90%. Lipid-poor angiomyolipoma had the highest mean absolute unenhanced attenuation (p < 0.01); absolute unenhanced attenuation greater than 45 HU and relative corticomedullary attenuation less than 10% differentiated lipid-poor angiomyolipoma from clear cell RCC with a negative predictive value of 97%. CONCLUSION: Four-phase MDCT renal attenuation profiles enable differentiation of clear cell RCC from other solid renal cortical masses, most notably papillary RCC and lipid-poor angiomyolipoma.

Efficacy of imaging-guided percutaneous radiofrequency ablation for the treatment of biopsy-proven malignant cystic renal masses.

OBJECTIVE: The purpose of this study was to determine the efficacy of imaging-guided percutaneous radiofrequency ablation (RFA) for the treatment of Bosniak category III and IV cystic renal lesions. MATERIALS AND METHODS: Our database was searched to assemble a cohort of biopsy-proven malignant Bosniak category III and IV cystic renal lesions that were treated with imaging-guided percutaneous RFA from 2004 to 2012. The clinical history, imaging features, procedural complications, pathologic results, imaging follow-up, and clinical outcomes of each case were reviewed. RESULTS: A total of 16 patients and 23 biopsy-proven malignant cystic renal lesions were included; two patients with von Hippel-Lindau syndrome had four and three treated lesions each, and a patient with multiple renal tumors had three treated lesions. The other 13 patients each had a single lesion. Clinical follow-up ranged from 2 to 110 months (average, 24 months). The primary treatment efficacy of RFA was 91% (21/23 lesions), and the secondary treatment efficacy was 96% (22/23 lesions). A minority of patients experienced partial loss of renal function. There were no complications related to bleeding or tumor seeding. CONCLUSION: Imaging-guided percutaneous RFA is safe and effective for the treatment of Bosniak category III and IV cystic renal lesions.