Computational studies of biological networks can help to identify components and wirings responsible for observed phenotypes. However, studying stochastic networks controlling many biological processes is challenging. Similar to Schrödinger's equation in quantum mechanics, the chemical master equation (CME) provides a basic framework for understanding stochastic networks. However, except for simple problems, the CME cannot be solved analytically. Here we use a method called discrete chemical master equation (dCME) to compute directly the full steady-state probability landscape of the lysogeny maintenance network in phage lambda from its CME. Results show that wild-type phage lambda can maintain a constant level of repressor over a wide range of repressor degradation rate and is stable against UV irradiation, ensuring heritability of the lysogenic state. Furthermore, it can switch efficiently to the lytic state once repressor degradation increases past a high threshold by a small amount. We find that beyond bistability and nonlinear dimerization, cooperativity between repressors bound to O R 1 and O R 2 is required for stable and heritable epigenetic state of lysogeny that can switch efficiently. Mutants of phage lambda lack stability and do not possess a high threshold. Instead, they are leaky and respond to gradual changes in degradation rate. Our computation faithfully reproduces the hair triggers for UVinduced lysis observed in mutants and the limitation in robustness against mutations. The landscape approach computed from dCME is general and can be applied to study broad issues in systems biology.B acteriophage lambda is a virus that infects Escherichia coli cells. It has served as a model system for studying regulatory networks and for engineering gene circuits (1-5). Of central importance is the molecular circuitry that controls phage lambda to choose between two productive modes of development, namely, the lysogenic state and the lytic state (Fig 1A). In the lysogenic state, phage lambda represses its developmental function, integrates its DNA into the chromosome of the host E. coli bacterium, and is replicated in cell cycles for potentially many generations. When threatening DNA damage occurs, phage lambda switches from the epigenetic state of lysogeny to the lytic state and undergoes massive replications in a single cell cycle, releases 50-100 progeny phages upon lysis of the E. coli cell. This switching process is called prophage induction (5).The molecular network that controls the choice between these two different physiological states has been studied extensively during the past 40 y (5-9). All of the major molecular components of the network have been identified, binding constants and reaction rates characterized, and there is a good experimental understanding of the general mechanism of the molecular switch (5). Theoretical studies have also contributed to the illumination of the central role of stochasticity (3) and the stability of lysogen against spontaneous switching (4, 10). With the advent o...

Breast cancer is the most commonly diagnosed cancer in women, with 10% of disease attributed to hereditary factors. Although BRCA1 and BRCA2 account for a high percentage of hereditary cases, there are more than 25 susceptibility genes that differentially impact the risk for breast cancer. Traditionally, germline testing for breast cancer was performed by Sanger dideoxy terminator sequencing in a reflexive manner, beginning with BRCA1 and BRCA2. The introduction of next-generation sequencing (NGS) has enabled the simultaneous testing of all genes implicated in breast cancer resulting in diagnostic labs offering large, comprehensive gene panels. However, some physicians prefer to only test for those genes in which established surveillance and treatment protocol exists. The NGS based BRCAplus test utilizes a custom tiled PCR based target enrichment design and bioinformatics pipeline coupled with array comparative genomic hybridization (aCGH) to identify mutations in the six high-risk genes: BRCA1, BRCA2, PTEN, TP53, CDH1, and STK11. Validation of the assay with 250 previously characterized samples resulted in 100% detection of 3,025 known variants and analytical specificity of 99.99%. Analysis of the clinical performance of the first 3,000 BRCAplus samples referred for testing revealed an average coverage greater than 9,000X per target base pair resulting in excellent specificity and the sensitivity to detect low level mosaicism and allele-drop out. The unique design of the assay enabled the detection of pathogenic mutations missed by previous testing. With the abundance of NGS diagnostic tests being released, it is essential that clinicians understand the advantages and limitations of different test designs.

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Objective: We describe a novel congenital motor neuron disease with early demise due to respiratory insufficiency with clinical overlap with spinal muscular atrophy with respiratory distress (SMARD) type 1 but lacking a mutation in the IGHMBP2 gene.Methods: Exome sequencing was used to identify a de novo mutation in the LAS1L gene in the proband. Pathogenicity of the mutation was validated using a zebrafish model by morpholinomediated knockdown of las1l.Results: We identified a de novo mutation in the X-linked LAS1L gene in the proband (p.S477N).The mutation is in a highly conserved region of the LAS1L gene predicted to be deleterious by bioinformatic analysis. Morpholino-based knockdown of las1l, the orthologous gene in zebrafish, results in early lethality and disruption of muscle and peripheral nerve architecture. Coinjection of wild-type but not mutant human RNA results in partial rescue of the phenotype. Conclusion:We report a patient with a SMARD phenotype due to a mutation in LAS1L, a gene important in coordinating processing of the 45S pre-rRNA and maturation of the large 60S ribosomal subunit. Similarly, the IGHMB2 gene associated with SMARD type 1 has been suggested to have an important role in ribosomal biogenesis from its role in processing the 45S pre-rRNA. We propose that disruption of ribosomal maturation may be a common pathogenic mechanism linking SMARD phenotypes caused by both IGHMBP2 and LAS1L. Spinal muscular atrophy with respiratory distress (SMARD) is a rare autosomal recessive disorder of neonatal weakness and early respiratory failure (Online Mendelian Inheritance in Man [OMIM] #604320). 1 SMARD was first described in 1974 as a variant of WerdnigHoffmann disease (spinal muscular atrophy type I) but is distinguished by the prominence of early respiratory failure and distal muscle weakness or joint contractures.2 Since discovery of the IGHMBP2 gene as a cause for SMARD, 3 appreciation of the clinical and genetic heterogeneity has been increasing.2,4,5 IGHMBP2 is a ubiquitously expressed helicase that colocalizes with factors controlling RNA splicing in the cytosol and nucleus. 6 A role for IGHMBP2 in translation has been proposed based on colocalization in the cytoplasm with ribosomal proteins and ribosomal RNA (rRNA). 6,7 As in many other disorders with motor neuron involvement, it is unclear why mutations in IGHMBP2 have a disproportionate effect on motor neurons. 8Infants presenting with a SMARD phenotype but lacking mutations in IGHMBP2 are common, accounting for up to two-thirds of reported patients. 4,9 We describe an infant who presented with distal weakness and primary respiratory failure associated with diaphragm paralysis but lacking a

PURPOSE The current diagnostic testing algorithm for Lynch syndrome (LS) is complex and often involves multiple follow-up germline and somatic tests. We aimed to describe the results of paired tumor/germline testing performed on a large cohort of patients with colorectal cancer (CRC) and endometrial cancer (EC) to better determine the utility of this novel testing methodology. MATERIALS AND METHODS We retrospectively reviewed a consecutive series of patients with CRC and EC undergoing paired tumor/germline analysis of the LS genes at a clinical diagnostic laboratory (N = 702). Microsatellite instability, MLH1 promoter hypermethylation, and germline testing of additional genes were performed if ordered. Patients were assigned to one of five groups on the basis of prior tumor screening and germline testing outcomes. Results for each group are described. RESULTS Overall results were informative regarding an LS diagnosis for 76.1% and 60.8% of patients with mismatch-repair–deficient (MMRd) CRC and EC without and with prior germline testing, respectively. LS germline mutations were identified in 24.8% of patients in the group without prior germline testing, and interestingly, in 9.5% of patients with previous germline testing; four of these were discordant with prior tumor screening. Upon excluding patients with MLH1 promoter hypermethylation and germline mutations, biallelic somatic inactivation was seen in approximately 50% of patients with MMRd tumors across groups. CONCLUSION Paired testing identified a cause for MMRd tumors in 76% and 61% of patients without and with prior LS germline testing, respectively. Findings support inclusion of tumor sequencing as well as comprehensive LS germline testing in the LS testing algorithm. Paired testing offers a complete, convenient evaluation for LS with high diagnostic resolution.

Clinical genetic testing for hereditary breast and ovarian cancer (HBOC) is becoming widespread. However, the interpretation of variants of unknown significance (VUS) in HBOC genes, such as the clinically actionable genes BRCA1 and BRCA2, remain a challenge. Among the variants that are frequently classified as VUS are those with unclear effects on splicing. In order to address this issue we developed a high-throughput RNA-massively parallel sequencing assay—CloneSeq—capable to perform quantitative and qualitative analysis of transcripts in cell lines and HBOC patients. This assay is based on cloning of RT-PCR products followed by massive parallel sequencing of the cloned transcripts. To validate this assay we compared it to the RNA splicing assays recommended by members of the ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) consortium. This comparison was performed using well-characterized lymphoblastoid cell lines (LCLs) generated from carriers of the BRCA1 or BRCA2 germline variants that have been previously described to be associated with splicing defects. CloneSeq was able to replicate the ENIGMA results, in addition to providing quantitative characterization of BRCA1 and BRCA2 germline splicing alterations in a high-throughput fashion. Furthermore, CloneSeq was used to analyze blood samples obtained from carriers of BRCA1 or BRCA2 germline sequence variants, including the novel uncharacterized alteration BRCA1 c.5152+5G>T, which was identified in a HBOC family. CloneSeq provided a high-resolution picture of all the transcripts induced by BRCA1 c.5152+5G>T, indicating it results in significant levels of exon skipping. This analysis proved to be important for the classification of BRCA1 c.5152+5G>T as a clinically actionable likely pathogenic variant. Reclassifications such as these are fundamental in order to offer preventive measures, targeted treatment, and pre-symptomatic screening to the correct individuals.

We investigate the transition energy of vertically coupled quantum dots and rings (VCQDs and VCQRs) with a three-dimensional (3D) model under an applied magnetic field. The model formulation includes (1) the position-dependent effective mass Hamiltonian in the nonparabolic approximation for electrons, (2) the position-dependent effective mass Hamiltonian in the parabolic approximation for holes, (3) the finite hard-wall confinement potential, and (4) the Ben Daniel-Duke boundary conditions. We explore small VCQDs and VCQRs with disk (DI) and conical (CO) shapes. For small VCQDs and VCQRs, the electron-hole transition energy is dominated by the interdistance d which plays a crucial role in the tunable states of structures. Under zero magnetic field, there is about 25% variation in the electron ground state energy for both InAs/GaAs DI-shaped VCQDs and VCQRs with d varying from 0.4 nm to 4.8 nm. The energy spectra of the CO-shaped VCQDs are the most stable against the structure interdistance deviations (among dots and rings of the same volume). For a fixed d, VCQDs show diamagnetic shift; contrarily, VCQRs imply a nonperiodical transition among the lowest electron energy states. The energy band gap of VCQRs oscillates nonperiodically between the lowest electron and holes states as a function of external magnetic fields. Our investigation is constructive for studying the magneto-optical phenomena of the nanoscale semiconductor artificial molecules.

We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of occupancy of all 802,075 conformations of 16-mers over 7-orders of time span. We find that (i) folding rates of these protein-like sequences of same length can differ by 4-orders of magnitude, (ii) folding rates of sequences of the same conformation can differ by a factor of 190, and (iii) parameters of the native structures, designability, and thermodynamic properties are weak predictors of the folding rates, rather, basin analysis of the kinematic energy landscape defined by the moves can provide excellent account of the observed folding rates.The dynamics of protein folding has been studied extensively [1,2]. A remarkable observation is that protein folding rates are well correlated with their native structural properties [1]. A native centric view postulates that protein folding rates are largely determined by the topology of its native structure [3]. Theoretical models using Gō potential where only native contacts contribute energetically are very successful in reproducing observed folding rates [2,4]. However, the extent to which native structure determines folding rate remains unclear. By the native-centric view, different sequences for the same protein structural fold would all have very similar folding rates, as they share essentially the same native structure topology. However, this is not consistent with experimental results. As the folding rates of simple single-domain proteins differ by 6 orders of magnitude [3], folding rates may be very heterogeneous. A recent experimental study showed that a designed artificial protein with no homologous sequence in nature that adopts the same structure as a natural protein can fold 4,000 times faster [5]. A distinct possibility is that the empirical correlation between properties of native protein structures and folding rates may arise from inadequate sampling in the sequence space due to accumulated biased natural selection and limited genetic drift, rather than from intrinsic physical properties of proteins.In this letter, we use two-dimensional hydrophobic and polar (HP) lattice model [6] to study the relationship of folding rates, native structure topology, thermodynamic properties, and effects of sequence variation. We model the physical movement of protein chains. Real protein cannot immediately jump from one conformation to another arbitrary conformation. Two conformations of the same energy may be well separated kinetically. We regard protein movement as a sequence of successive conformational changes, each represented by a physically realizable primitive move. The physical move set we developed exhausts all possible conformational changes for a structure. We use master equation to study the folding dynamics of foldable sequences of length 16. While master equation provides an exact solution [6,7], in the past it was neces...