Animal models of Down syndrome (DS), trisomic for human chromosome 21 (HSA21) genes or orthologs,... more Animal models of Down syndrome (DS), trisomic for human chromosome 21 (HSA21) genes or orthologs, provide insights into better understanding and treatment options. The only existing transchromosomic (Tc) mouse DS model, Tc1, carries a HSA21 with over 50 protein coding genes (PCGs) disrupted. Tc1 is mosaic, compromising interpretation of results. Here, we "clone" the 34 MB long arm of HSA21 (HSA21q) as a mouse artificial chromosome (MAC). Through multiple steps of microcell-mediated chromosome transfer, we created a new Tc DS mouse model, Tc (HSA21q;MAC)1Yakaz ("TcMAC21"). TcMAC21 is not mosaic and contains 93% of HSA21q PCGs that are expressed and regulatable. TcMAC21 recapitulates many DS phenotypes including anomalies in heart, craniofacial skeleton and brain, molecular/cellular pathologies, and impairments
Dysregulation of Sonic hedgehog (SHH) signaling may contribute to multiple Down syndrome-associat... more Dysregulation of Sonic hedgehog (SHH) signaling may contribute to multiple Down syndrome-associated phenotypes, including cerebellar hypoplasia, congenital heart defects, craniofacial and skeletal dysmorphologies, and Hirschsprung disease. Granule cell precursors isolated from the developing cerebellum of Ts65Dn mice are less responsive to the mitogenic effects of SHH than euploid cells, and a single postnatal dose of the SHH pathway agonist SAG rescues cerebellar morphology and performance on learning and memory tasks in Ts65Dn mice. SAG treatment also normalizes expression levels of OLIG2 in neural progenitor cells derived from human trisomy 21 iPSCs. However, despite evidence that activating SHH signaling can ameliorate some Down syndrome-associated phenotypes, chromosome 21 does not encode any components of the canonical SHH pathway. Here, we screened 163 chromosome 21 cDNAs in a series of SHH-responsive cell lines to identify chromosome 21 genes that modulate SHH signaling. We ...
Next generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of trans... more Next generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, due to the variation in gene expression levels and alternative splicing. We developed a k-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted k-mers in the input reads. Unlike WGS read correctors, which employ a global threshold to determine trusted k-mers, Rcorrector computes a local threshold at every position in a read. The software as published is available directly from here, but for the most up to date version please see the project GitHub https://github.com/mourisl/Rcorrector/ repository.
Animal models of Down syndrome (DS), trisomic for human chromosome 21 (HSA21) genes or orthologs,... more Animal models of Down syndrome (DS), trisomic for human chromosome 21 (HSA21) genes or orthologs, provide insights into better understanding and treatment options. The only existing transchromosomic (Tc) mouse DS model, Tc1, carries a HSA21 with over 50 protein coding genes (PCGs) disrupted. Tc1 is mosaic, compromising interpretation of results. Here, we “clone” the 34 MB long arm of HSA21 (HSA21q) as a mouse artificial chromosome (MAC). Through multiple steps of microcell-mediated chromosome transfer, we created a new Tc DS mouse model, Tc(HSA21q;MAC)1Yakaz (“TcMAC21”). TcMAC21 is not mosaic and contains 93% of HSA21q PCGs that are expressed and regulatable. TcMAC21 recapitulates many DS phenotypes including anomalies in heart, craniofacial skeleton and brain, molecular/cellular pathologies, and impairments in learning, memory and synaptic plasticity. TcMAC21 is the most complete genetic mouse model of DS extant and has potential for supporting a wide range of basic and preclinical...
Transcript assembly from RNA-seq reads is a critical step in gene expression and subsequent funct... more Transcript assembly from RNA-seq reads is a critical step in gene expression and subsequent functional analyses. Here we present PsiCLASS, an accurate and efficient transcript assembler based on an approach that simultaneously analyzes multiple RNA-seq samples. PsiCLASS combines mixture statistical models for exonic feature selection across multiple samples with splice graph based dynamic programming algorithms and a weighted voting scheme for transcript selection. PsiCLASS achieves significantly better sensitivity-precision tradeoff, and renders precision up to 2-3 fold higher than the StringTie system and Scallop plus TACO, the two best current approaches. PsiCLASS is efficient and scalable, assembling 667 GEUVADIS samples in 9 h, and has robust accuracy with large numbers of samples.
We set out to develp novel workflows to identify panels of methylated human papilloma virus (HPV)... more We set out to develp novel workflows to identify panels of methylated human papilloma virus (HPV) and human genes that can discriminate between CIN2+ and normal/CIN1 patients in liquid prep samples and in Transrenal DNA (TrDNA) isolated from urine. Using Human DNA methylation arrays and massively parallel Next Generation Sequencing (NGS) for Discovery and quantitative Methylation Specific PCR (qMSP) for validation, we found that promoter methylation of ZNF516, FKBP6, and INST1 discriminates samples with CIN2+ lesions from no intraepithelial lesions or malignancy (NILM) in cervical brush samples: 88.3% sensitivity, 88.9% specificity, 93.2 Area Under the Curve (AUC), 86.9% positive predictive value (PPV) and 90.2% negative predictive value (NPV). Using custom sequence capture pools of baits, we pulled down genomic and bisulfite converted high-risk HPV DNA before library prep for massively parallel Next Generation Sequencing (NGS) in 454 and MiSeq instruments, respectively to identify ...
2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2016
Accurate alternative splicing detection and transcript reconstruction are essential to characteri... more Accurate alternative splicing detection and transcript reconstruction are essential to characterize gene regulation and function and to understand development and disease. However, current methods for extracting splicing variation from RNA-seq data only analyze signals from a single sample, which limits transcript reconstruction and fails to detect a complete set of alternative splicing events. We developed a novel feature selection method, JULiP, that analyzes information across multiple samples to identify alternative splicing variation in the form of splice junctions (introns). It formulates the selection problem as a regularized program, utilizing the latent information from multiple RNA-seq samples to construct an accurate and comprehensive intron set. JULiP is highly accurate, and could detect thousands more introns in any one sample, >30% more than the most sensitive single-sample method, and 10% more introns than in the cumulative set of samples, at higher or comparable p...
BACKGROUND. Germline mutations in telomerase and other telomere maintenance genes manifest in the... more BACKGROUND. Germline mutations in telomerase and other telomere maintenance genes manifest in the premature aging short telomere syndromes. Myelodysplastic syndromes and acute myeloid leukemia (MDS/AML) account for 75% of associated malignancies, but how these cancers overcome the inherited telomere defect is unknown. METHODS. We used ultra-deep targeted sequencing to detect somatic reversion mutations in 17 candidate telomere lengthening genes among controls and patients with short telomere syndromes with and without MDS/AML, and we tested the functional significance of these mutations. RESULTS. While no controls carried somatic mutations in telomere maintenance genes, 29% (16 of 56) of adults with germline telomere maintenance defects carried at least 1 (P < 0.001), and 13% (7 of 56) had 2 or more. In addition to TERT promoter mutations, which were present in 19%, another 13% of patients carried a mutation in POT1 or TERF2IP. POT1 mutations impaired telomere binding in vitro and some mutations were identical to ones seen in familial melanoma associated with longer telomere length. Exclusively in patients with germline defects in telomerase RNA (TR), we identified somatic mutations in nuclear RNA exosome genes RBM7, SKIV2L2, and DIS3, where loss-of-function upregulates mature TR levels. Somatic reversion events in 6 telomere-related genes were more prevalent in patients who were MDS/AML-free (P = 0.02, RR 4.4, 95% CI 1.2-16.7), and no patient with MDS/AML had more than 1 reversion mutation. CONCLUSION. Our data indicate that diverse adaptive somatic mutations arise in the short telomere syndromes. Their presence may alleviate the telomere crisis that promotes transformation to MDS/AML.
BAM alignment files of simulated RNA-seq data used to evaluate PsiCLASS and other transcript asse... more BAM alignment files of simulated RNA-seq data used to evaluate PsiCLASS and other transcript assemblers (archive contains 25 files).
The cytokine interleukin-6 (IL-6) has pleiotropic effects in aging and is elevated in frail older... more The cytokine interleukin-6 (IL-6) has pleiotropic effects in aging and is elevated in frail older adults. We have developed a conditional mouse model to better characterize the role of IL-6 in promoting frailty and age-related mitochondrial dysregulation. The human IL-6 (hIL-6) knock-in mouse (TetO-hIL6) was developed utilizing CRISPR/Cas9 technology with transgene donor vector containing a tetracycline response element promoter driving expression of hIL-6 cDNA. Male TetO-hIL6 mice were treated with doxycycline-containing water for six weeks starting at 8 months old. RNAseq analysis of whole blood demonstrated significant upregulation of pro-inflammatory related markers at 6 weeks compared to baseline and upregulated cell proliferation and metabolism pathways. Physical testing of TetO-hIL6 mice before and after hIL-6 induction demonstrated decreased grip strength (p =0.003), decreased running capacity (p = 0.02), and 40% increase in falls off of the treadmill (p = 0.001). Induced mi...
Inherited mutations in telomerase and other telomere maintenance genes manifest in the premature ... more Inherited mutations in telomerase and other telomere maintenance genes manifest in the premature aging short telomere syndromes. Myelodysplastic syndromes and acute myeloid leukemia (MDS/AML) account for 75% of associated malignancies, but how these cancers overcome the germline telomere defect is unknown. We used targeted ultra-deep sequencing to detect candidate somatic reversion mutations hypothesizing they may promote MDS/AML evolution. While no controls carried somatic mutations in telomere maintenance genes (0 of 28), 29% of adults with germline telomere maintenance defects carried at least one (16 of 56, P<0.001). In addition to TERT promoter mutations which were present in 19%, we identified POT1 and TERF2IP mutations in 13%. POT1 mutations impaired telomere binding and in some cases were identical to those found in familial melanoma associated with longer telomere length. Exclusively in patients with germline defects in telomerase RNA (TR), we identified somatic mutation...
Motivation Gene alternative splicing plays an important role in development, tissue specializatio... more Motivation Gene alternative splicing plays an important role in development, tissue specialization and disease and differences in splicing patterns can reveal important factors for phenotypic differentiation. While multiple computational methods exist to determine splicing differences, there is a need for user-friendly visualizations that present an intuitive view of the data and work across methods. Results We developed a toolkit, Jutils, for visualizing differential splicing events at the intron (splice junction) level. Jutils is method-agnostic, converting individual tools’ output into a unified representation and using it to create visualizations. Jutils creates three types of visualizations, namely heatmaps of absolute and Z-score normalized splice ratios, sashimi plots and Venn diagrams of results from multiple comparisons. Jutils is lightweight, relying solely on the unified data file for visualizations. Availability and implementation Jutils is implemented in Python and is a...
Alternative splicing of mRNA is an essential gene regulatory mechanism with important roles in de... more Alternative splicing of mRNA is an essential gene regulatory mechanism with important roles in development and disease. We present MntJULiP, a method for comprehensive and accurate quantification of splicing differences between two or more conditions. MntJULiP implements novel Dirichlet-multinomial and zero-inflated negative binomial models within a Bayesian framework to detect both changes in splicing ratios and in absolute splicing levels of introns with high accuracy, and can find classes of variation overlooked by reference tools. Additionally, a mixture model allows multiple conditions to be compared simultaneously. Highly scalable, it processed hundreds of GTEx samples in <1 hour to reveal splicing constituents of tissue differentiation.
All procedures performed in studies involving human participants were in accordance with the ethi... more All procedures performed in studies involving human participants were in accordance with the ethical standards of the Johns Hopkins institutional review board and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Written informed consent was obtained from all individual participants included in the study.
Journal of the American Academy of Dermatology, 2020
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
This study confirms several novel cancer-specific ASEs in HPV+OPSCC. In addition, chromatin modif... more This study confirms several novel cancer-specific ASEs in HPV+OPSCC. In addition, chromatin modifications regulate xpression of aberrant tumor specific splice variants, and modulation of chromatin structure resulted in growth inhibition in an ASE-rich in vitro odel.
Background: Associations between acne and gastrointestinal comorbidities suggest that microbial d... more Background: Associations between acne and gastrointestinal comorbidities suggest that microbial dysbiosis and intestinal permeability may promote inflammatory acne, a condition often managed with oral antibiotics. Objective: We performed a case-control study to investigate the skin and gut microbiota in 8 acne patients before and after receiving oral minocycline compared to controls matched by age ±5 years, sex, and race. Methods: DNA was extracted from stool samples and facial skin swabs. Sequencing of the V3V4 region of the bacterial 16S rRNA gene was performed using Illumina MiSeq and analyzed using QIIME/MetaStats 2.0 software. Results: Acne patients included 7 female and 1 male, ages 20∼ 32. Shannon diversity was not significantly different between the skin (p=0.153) or gut (p<0.999) microbiota of acne patients before and after antibiotics. The gut microbiota in pre-antibiotic acne patients compared to acne-free controls was depleted in probiotics Lactobacillus iners (p=0.001), Lactobacillus zeae (p=0.001), and Bifidobacterium animalis (p=0.026). After antibiotics, the gut microbiota of acne patients was depleted in Lactobacillus salivar-ius (p=0.001), Bifidobacterium adolescentis (p=0.002), Bifidobacterium pseudolongum (p=0.010), and Bifidobacterium breve (p=0.042), while the skin microbiota was enriched in probiotics Bifidobacterium longum (p=0.028) and Leuconostoc mesenteroides (p=0.029) and depleted in Staphylococcus epidermidis (p=0.009) and Prevotella nigrescens (p=0.028). At the phylum level, significant enrichment of Bacteroidetes in stool of acne patients following antibiotic treatment (p=0.033) led to a decreased Firmicutes to Bacteroidetes ratio. Conclusion: Minocycline produces significant derangements in the microbiota of the skin and gut, including many probiotic species, highlighting the potential for more targeted antimicrobial treatments for acne. (Ann Dermatol 32(1) 21∼30, 2020
Animal models of Down syndrome (DS), trisomic for human chromosome 21 (HSA21) genes or orthologs,... more Animal models of Down syndrome (DS), trisomic for human chromosome 21 (HSA21) genes or orthologs, provide insights into better understanding and treatment options. The only existing transchromosomic (Tc) mouse DS model, Tc1, carries a HSA21 with over 50 protein coding genes (PCGs) disrupted. Tc1 is mosaic, compromising interpretation of results. Here, we "clone" the 34 MB long arm of HSA21 (HSA21q) as a mouse artificial chromosome (MAC). Through multiple steps of microcell-mediated chromosome transfer, we created a new Tc DS mouse model, Tc (HSA21q;MAC)1Yakaz ("TcMAC21"). TcMAC21 is not mosaic and contains 93% of HSA21q PCGs that are expressed and regulatable. TcMAC21 recapitulates many DS phenotypes including anomalies in heart, craniofacial skeleton and brain, molecular/cellular pathologies, and impairments
Dysregulation of Sonic hedgehog (SHH) signaling may contribute to multiple Down syndrome-associat... more Dysregulation of Sonic hedgehog (SHH) signaling may contribute to multiple Down syndrome-associated phenotypes, including cerebellar hypoplasia, congenital heart defects, craniofacial and skeletal dysmorphologies, and Hirschsprung disease. Granule cell precursors isolated from the developing cerebellum of Ts65Dn mice are less responsive to the mitogenic effects of SHH than euploid cells, and a single postnatal dose of the SHH pathway agonist SAG rescues cerebellar morphology and performance on learning and memory tasks in Ts65Dn mice. SAG treatment also normalizes expression levels of OLIG2 in neural progenitor cells derived from human trisomy 21 iPSCs. However, despite evidence that activating SHH signaling can ameliorate some Down syndrome-associated phenotypes, chromosome 21 does not encode any components of the canonical SHH pathway. Here, we screened 163 chromosome 21 cDNAs in a series of SHH-responsive cell lines to identify chromosome 21 genes that modulate SHH signaling. We ...
Next generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of trans... more Next generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, due to the variation in gene expression levels and alternative splicing. We developed a k-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted k-mers in the input reads. Unlike WGS read correctors, which employ a global threshold to determine trusted k-mers, Rcorrector computes a local threshold at every position in a read. The software as published is available directly from here, but for the most up to date version please see the project GitHub https://github.com/mourisl/Rcorrector/ repository.
Animal models of Down syndrome (DS), trisomic for human chromosome 21 (HSA21) genes or orthologs,... more Animal models of Down syndrome (DS), trisomic for human chromosome 21 (HSA21) genes or orthologs, provide insights into better understanding and treatment options. The only existing transchromosomic (Tc) mouse DS model, Tc1, carries a HSA21 with over 50 protein coding genes (PCGs) disrupted. Tc1 is mosaic, compromising interpretation of results. Here, we “clone” the 34 MB long arm of HSA21 (HSA21q) as a mouse artificial chromosome (MAC). Through multiple steps of microcell-mediated chromosome transfer, we created a new Tc DS mouse model, Tc(HSA21q;MAC)1Yakaz (“TcMAC21”). TcMAC21 is not mosaic and contains 93% of HSA21q PCGs that are expressed and regulatable. TcMAC21 recapitulates many DS phenotypes including anomalies in heart, craniofacial skeleton and brain, molecular/cellular pathologies, and impairments in learning, memory and synaptic plasticity. TcMAC21 is the most complete genetic mouse model of DS extant and has potential for supporting a wide range of basic and preclinical...
Transcript assembly from RNA-seq reads is a critical step in gene expression and subsequent funct... more Transcript assembly from RNA-seq reads is a critical step in gene expression and subsequent functional analyses. Here we present PsiCLASS, an accurate and efficient transcript assembler based on an approach that simultaneously analyzes multiple RNA-seq samples. PsiCLASS combines mixture statistical models for exonic feature selection across multiple samples with splice graph based dynamic programming algorithms and a weighted voting scheme for transcript selection. PsiCLASS achieves significantly better sensitivity-precision tradeoff, and renders precision up to 2-3 fold higher than the StringTie system and Scallop plus TACO, the two best current approaches. PsiCLASS is efficient and scalable, assembling 667 GEUVADIS samples in 9 h, and has robust accuracy with large numbers of samples.
We set out to develp novel workflows to identify panels of methylated human papilloma virus (HPV)... more We set out to develp novel workflows to identify panels of methylated human papilloma virus (HPV) and human genes that can discriminate between CIN2+ and normal/CIN1 patients in liquid prep samples and in Transrenal DNA (TrDNA) isolated from urine. Using Human DNA methylation arrays and massively parallel Next Generation Sequencing (NGS) for Discovery and quantitative Methylation Specific PCR (qMSP) for validation, we found that promoter methylation of ZNF516, FKBP6, and INST1 discriminates samples with CIN2+ lesions from no intraepithelial lesions or malignancy (NILM) in cervical brush samples: 88.3% sensitivity, 88.9% specificity, 93.2 Area Under the Curve (AUC), 86.9% positive predictive value (PPV) and 90.2% negative predictive value (NPV). Using custom sequence capture pools of baits, we pulled down genomic and bisulfite converted high-risk HPV DNA before library prep for massively parallel Next Generation Sequencing (NGS) in 454 and MiSeq instruments, respectively to identify ...
2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2016
Accurate alternative splicing detection and transcript reconstruction are essential to characteri... more Accurate alternative splicing detection and transcript reconstruction are essential to characterize gene regulation and function and to understand development and disease. However, current methods for extracting splicing variation from RNA-seq data only analyze signals from a single sample, which limits transcript reconstruction and fails to detect a complete set of alternative splicing events. We developed a novel feature selection method, JULiP, that analyzes information across multiple samples to identify alternative splicing variation in the form of splice junctions (introns). It formulates the selection problem as a regularized program, utilizing the latent information from multiple RNA-seq samples to construct an accurate and comprehensive intron set. JULiP is highly accurate, and could detect thousands more introns in any one sample, >30% more than the most sensitive single-sample method, and 10% more introns than in the cumulative set of samples, at higher or comparable p...
BACKGROUND. Germline mutations in telomerase and other telomere maintenance genes manifest in the... more BACKGROUND. Germline mutations in telomerase and other telomere maintenance genes manifest in the premature aging short telomere syndromes. Myelodysplastic syndromes and acute myeloid leukemia (MDS/AML) account for 75% of associated malignancies, but how these cancers overcome the inherited telomere defect is unknown. METHODS. We used ultra-deep targeted sequencing to detect somatic reversion mutations in 17 candidate telomere lengthening genes among controls and patients with short telomere syndromes with and without MDS/AML, and we tested the functional significance of these mutations. RESULTS. While no controls carried somatic mutations in telomere maintenance genes, 29% (16 of 56) of adults with germline telomere maintenance defects carried at least 1 (P < 0.001), and 13% (7 of 56) had 2 or more. In addition to TERT promoter mutations, which were present in 19%, another 13% of patients carried a mutation in POT1 or TERF2IP. POT1 mutations impaired telomere binding in vitro and some mutations were identical to ones seen in familial melanoma associated with longer telomere length. Exclusively in patients with germline defects in telomerase RNA (TR), we identified somatic mutations in nuclear RNA exosome genes RBM7, SKIV2L2, and DIS3, where loss-of-function upregulates mature TR levels. Somatic reversion events in 6 telomere-related genes were more prevalent in patients who were MDS/AML-free (P = 0.02, RR 4.4, 95% CI 1.2-16.7), and no patient with MDS/AML had more than 1 reversion mutation. CONCLUSION. Our data indicate that diverse adaptive somatic mutations arise in the short telomere syndromes. Their presence may alleviate the telomere crisis that promotes transformation to MDS/AML.
BAM alignment files of simulated RNA-seq data used to evaluate PsiCLASS and other transcript asse... more BAM alignment files of simulated RNA-seq data used to evaluate PsiCLASS and other transcript assemblers (archive contains 25 files).
The cytokine interleukin-6 (IL-6) has pleiotropic effects in aging and is elevated in frail older... more The cytokine interleukin-6 (IL-6) has pleiotropic effects in aging and is elevated in frail older adults. We have developed a conditional mouse model to better characterize the role of IL-6 in promoting frailty and age-related mitochondrial dysregulation. The human IL-6 (hIL-6) knock-in mouse (TetO-hIL6) was developed utilizing CRISPR/Cas9 technology with transgene donor vector containing a tetracycline response element promoter driving expression of hIL-6 cDNA. Male TetO-hIL6 mice were treated with doxycycline-containing water for six weeks starting at 8 months old. RNAseq analysis of whole blood demonstrated significant upregulation of pro-inflammatory related markers at 6 weeks compared to baseline and upregulated cell proliferation and metabolism pathways. Physical testing of TetO-hIL6 mice before and after hIL-6 induction demonstrated decreased grip strength (p =0.003), decreased running capacity (p = 0.02), and 40% increase in falls off of the treadmill (p = 0.001). Induced mi...
Inherited mutations in telomerase and other telomere maintenance genes manifest in the premature ... more Inherited mutations in telomerase and other telomere maintenance genes manifest in the premature aging short telomere syndromes. Myelodysplastic syndromes and acute myeloid leukemia (MDS/AML) account for 75% of associated malignancies, but how these cancers overcome the germline telomere defect is unknown. We used targeted ultra-deep sequencing to detect candidate somatic reversion mutations hypothesizing they may promote MDS/AML evolution. While no controls carried somatic mutations in telomere maintenance genes (0 of 28), 29% of adults with germline telomere maintenance defects carried at least one (16 of 56, P<0.001). In addition to TERT promoter mutations which were present in 19%, we identified POT1 and TERF2IP mutations in 13%. POT1 mutations impaired telomere binding and in some cases were identical to those found in familial melanoma associated with longer telomere length. Exclusively in patients with germline defects in telomerase RNA (TR), we identified somatic mutation...
Motivation Gene alternative splicing plays an important role in development, tissue specializatio... more Motivation Gene alternative splicing plays an important role in development, tissue specialization and disease and differences in splicing patterns can reveal important factors for phenotypic differentiation. While multiple computational methods exist to determine splicing differences, there is a need for user-friendly visualizations that present an intuitive view of the data and work across methods. Results We developed a toolkit, Jutils, for visualizing differential splicing events at the intron (splice junction) level. Jutils is method-agnostic, converting individual tools’ output into a unified representation and using it to create visualizations. Jutils creates three types of visualizations, namely heatmaps of absolute and Z-score normalized splice ratios, sashimi plots and Venn diagrams of results from multiple comparisons. Jutils is lightweight, relying solely on the unified data file for visualizations. Availability and implementation Jutils is implemented in Python and is a...
Alternative splicing of mRNA is an essential gene regulatory mechanism with important roles in de... more Alternative splicing of mRNA is an essential gene regulatory mechanism with important roles in development and disease. We present MntJULiP, a method for comprehensive and accurate quantification of splicing differences between two or more conditions. MntJULiP implements novel Dirichlet-multinomial and zero-inflated negative binomial models within a Bayesian framework to detect both changes in splicing ratios and in absolute splicing levels of introns with high accuracy, and can find classes of variation overlooked by reference tools. Additionally, a mixture model allows multiple conditions to be compared simultaneously. Highly scalable, it processed hundreds of GTEx samples in <1 hour to reveal splicing constituents of tissue differentiation.
All procedures performed in studies involving human participants were in accordance with the ethi... more All procedures performed in studies involving human participants were in accordance with the ethical standards of the Johns Hopkins institutional review board and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Written informed consent was obtained from all individual participants included in the study.
Journal of the American Academy of Dermatology, 2020
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
This study confirms several novel cancer-specific ASEs in HPV+OPSCC. In addition, chromatin modif... more This study confirms several novel cancer-specific ASEs in HPV+OPSCC. In addition, chromatin modifications regulate xpression of aberrant tumor specific splice variants, and modulation of chromatin structure resulted in growth inhibition in an ASE-rich in vitro odel.
Background: Associations between acne and gastrointestinal comorbidities suggest that microbial d... more Background: Associations between acne and gastrointestinal comorbidities suggest that microbial dysbiosis and intestinal permeability may promote inflammatory acne, a condition often managed with oral antibiotics. Objective: We performed a case-control study to investigate the skin and gut microbiota in 8 acne patients before and after receiving oral minocycline compared to controls matched by age ±5 years, sex, and race. Methods: DNA was extracted from stool samples and facial skin swabs. Sequencing of the V3V4 region of the bacterial 16S rRNA gene was performed using Illumina MiSeq and analyzed using QIIME/MetaStats 2.0 software. Results: Acne patients included 7 female and 1 male, ages 20∼ 32. Shannon diversity was not significantly different between the skin (p=0.153) or gut (p<0.999) microbiota of acne patients before and after antibiotics. The gut microbiota in pre-antibiotic acne patients compared to acne-free controls was depleted in probiotics Lactobacillus iners (p=0.001), Lactobacillus zeae (p=0.001), and Bifidobacterium animalis (p=0.026). After antibiotics, the gut microbiota of acne patients was depleted in Lactobacillus salivar-ius (p=0.001), Bifidobacterium adolescentis (p=0.002), Bifidobacterium pseudolongum (p=0.010), and Bifidobacterium breve (p=0.042), while the skin microbiota was enriched in probiotics Bifidobacterium longum (p=0.028) and Leuconostoc mesenteroides (p=0.029) and depleted in Staphylococcus epidermidis (p=0.009) and Prevotella nigrescens (p=0.028). At the phylum level, significant enrichment of Bacteroidetes in stool of acne patients following antibiotic treatment (p=0.033) led to a decreased Firmicutes to Bacteroidetes ratio. Conclusion: Minocycline produces significant derangements in the microbiota of the skin and gut, including many probiotic species, highlighting the potential for more targeted antimicrobial treatments for acne. (Ann Dermatol 32(1) 21∼30, 2020
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