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PubMed2026

ALPINE: a scalable pipeline for comprehensive classification of gene-editing outcomes from long-read amplicon sequencing.

SUMMARY: CRISPR genome editing has enabled precise genetic modification for gene and cell therapies, but edits often produce heterogeneous on-target outcomes, including homology-directed repair (HDR) knock-ins, DNA repair template integrations, and structural variants. Existing tools are frequently limited to short reads or lack viral vector-specific integration categories needed for therapeutic development. Here, we present ALPINE (Amplicon Long-read Pipeline for INtegration Evaluation), a scalable and reproducible pipeline for classifying and quantifying gene-editing outcomes from long-read amplicon sequencing supporting both PacBio HiFi and Oxford Nanopore platforms. ALPINE classifies reads into 10+ categories, including DNA repair vector integration subtypes, and performs variant calling near the gene-edited site with batch, multi-sample reporting. Uniquely, ALPINE can distinguish between cells treated with multiple DNA repair vectors and identify distinct molecular features, such as inverted terminal repeats (ITRs), enabling comprehensive characterization of complex gene editing outcomes. Dual-target benchmarking on simulated datasets demonstrated high accuracy for transgene integration events. Independent validation on public crosslinked-HDR dataset confirmed ALPINE's integration detection capabilities, and application to edited T cell samples demonstrated comprehensive gene-editing outcome profiling. AVAILABILITY: ALPINE is available under MIT license at https://github.com/Maggi-Chen/ALPINE and https://doi.org/10.5281/zenodo.20272510. All analysis scripts and visualization code used in this manuscript are available at https://github.com/Maggi-Chen/ALPINE-manuscript-analysis. Simulated datasets are deposited at Zenodo (https://doi.org/10.5281/zenodo.20260865). Public dataset PRJNA913199 is available through NCBI SRA.

Gene Editing↗
PubMedDate not supplied

[New morphological data on multiple sclerosis].

The brain from 6 patients who died of multiple sclerosis was studied with MR tomography (MRT), macroscopy, light (CD 3, CD 20, LCA antigens) and electron microscopy (EM). Typical foci of demyelinization (plaques) were found in all cases. Alterations of brain arteries were found particularly in arteries of narrow lumen--with disturbance or even absence of elastin and muscle layer. Up to 30% of the vessels were surrounded by microcavities. Perivascular infiltrates consisting primarily of T lymphocytes were observed around the vessels (up to 70% of all vessels). This indicates the importance of vascular changes in the disease pathogenesis. Four variants of demyelinization (plaques) are distinguished depending on the degree of destruction of myelin, axons and glia. Two types of cells were found in the plaques with most pronounced changes: astrocytes and newly formed oligodendrocytes. Classification of plaques is suggested.

Adolescent↗
PubMed1978

The histopathological spectrum of nasopharyngeal carcinoma.

Nonglandular carcinomas of the nasopharynx originate in the epithelium of that anatomical region. Although numerous morphological patterns exist at the level observable by light microscopy, ultrastructurally, all have features of squamous-cell carcinoma. The most useful and consistent classification on the basis of light microscopy is that which separates keratinizing squamous carcinomas from nonkeratinizing carcinomas. Approximately 25% of tumours have abundant and easily recognized keratin. The nonkeratinizing types are more confusing, since many variants exist, both from tumour to tumour and, frequently, within the same tumour. Variable tissue reactions to infiltrating tumours, ranging from marked desmoplasia to complete absence of reaction, add to the confusion. The descriptive names applied to the variants of nonkeratinizing squamous carcinomas are well engraved in medical communications, and there is little chance that they will be abandoned.

Carcinoma↗
PubMed2026

Monogenic ALB Variants as Determinants of Severe Hypercholesterolemia: A Population-Based Cohort Study.

BACKGROUND: Hypoalbuminemia is associated with several risk factors for myocardial infarction, including hypercholesterolemia, liver disease, kidney disease, and diabetes. Homozygosity of loss-of-function (LoF) variants in the ALB gene, which encodes albumin, is a known cause of congenital hypoalbuminemia. Studies have also shown that heterozygous ALB LoF variants are associated with increases in low-density lipoprotein cholesterol (LDL-C), comparable to those seen in familial hypercholesterolemia. OBJECTIVES: This study examined the effect of ALB LoF variants and other causes of low albumin on LDL-C levels in 2 population biobanks. METHODS: This study used data from 2 large cohorts with linked electronic health record and genetic information: Geisinger's MyCode Community Health Initiative, a health care population based in Pennsylvania, USA; and the National Institutes of Health All of Us Research Program, a nationwide epidemiologic cohort. LDL-C values were adjusted for lipid-lowering medication use. Myocardial infarction diagnoses were extracted from electronic health records using International Classification of Diseases codes. A polygenic score for serum albumin was calculated for participants of European ancestry. Linear regression models were used to estimate associations, and results were meta-analyzed across cohorts using fixed-effects models. RESULTS: Among 155,530 MyCode and 405,701 All of Us adult participants, 77 individuals (1 of 7,289) carried an ALB LoF variant. Among noncarriers, a 1 g/dL decrease in serum albumin was associated with a 10.9 mg/dL (95% CI:, 10.4-11.4) decrease in LDL-C. In contrast, ALB LoF variants were associated with a 0.69 g/dL (95% CI: 0.60-0.78) reduction in serum albumin and a 38.3 mg/dL (95% CI: 28.2-48.5) increase in LDL-C. Paradoxically, whereas monogenic determinants of hypoalbuminemia were associated with increased LDL-C, polygenic determinants of lower albumin were associated with a 0.22 mg/dL (95% CI: 0.17-0.26) decrease in LDL-C per decile. CONCLUSIONS: ALB LoF variants represent a previously underrecognized monogenic cause of elevated LDL-C, with effect sizes slightly less than canonical familial hypercholesterolemia variants. The divergent effects of ALB-mediated vs polygenic or physiological reductions in albumin on LDL-C suggest distinct underlying mechanisms.

Humans↗
PubMed1999

The classification, recognition and significance of polyagglutination in transfusion medicine.

Polyagglutination, although an uncommon phenomenon in transfusion medicine, is becoming increasingly recognized as a potential pitfall in correct ABO typing and can hinder the rapid allocation of accurately crossmatched blood products. Polyagglutination refers to erythrocytes which demonstrate agglutination with the majority of adult sera upon initial ABO crossmatch testing. Most types of polyagglutination involve alteration of red cell surface antigens through microbial enzymatic activity in patients with sepsis, and subsequent interaction of these newly exposed 'cryptantigens' with naturally occuring IgM antibody which is present in most adult sera. Less common variants include essential inborn variations in red cell development, and have been associated with myelodysplastic syndromes, congenital anemias, and various leukemias; it has been suggested that patients shown to possess these types of polyagglutination may benefit from increased hematologic surveillance. Recognition of polyagglutination in these settings is important to allow successful resolution of ABO typing discrepancies and permit efficient administration of appropriate blood products to these patients, who are often quite ill. The classification and method of laboratory recognition of polyagglutination is reviewed.

Adult↗
PubMed1998

Immunological and molecular characterization of three variant subtype P1.14 strains of Neisseria meningitidis.

Epidemic outbreaks of group B meningococcal disease exhibit a clonal nature consisting of a common serotype-subtype. Subtype-specific monoclonal antibodies (MAbs) directed toward two variable regions (VR1 and VR2) of the class 1 protein of Neisseria meningitidis are used in this classification scheme. A new MAb was developed to classify a nonsubtypeable (NST) strain of N. meningitidis, 7967. This MAb bound to both the NST strain and the prototype subtype P1. 14 strain, S3446, by dot blot analysis. However, a MAb produced to the prototype P1.14 strain did not bind to strain 7967. Sixteen additional strains were further identified as P1.14 with the prototype MAb; of these, 15 strains bound both MAbs. Differences in the characteristics of binding of both antibodies to the three apparently diverse P1.14 strains were studied further by using outer membrane complex proteins, immobilized peptides, and soluble peptides. Deduced amino acid analysis suggested that both MAbs bind to VR2 and that single amino acid changes within VR2 (KM, NM, or KK) might explain the differences in binding characteristics. These results demonstrated that minor variations which exist within subtype variable regions may be clearly identified only by a combination of molecular and immunologic testing. The impact of subtype variation will become more evident as subtype-specific vaccines are developed and tested for efficacy.

Amino Acid Sequence↗
PubMed1987

Myeloproliferative disease in the dog and cat: definition, aetiology and classification.

The term myeloproliferative disease may be applied to all the non-lymphoid dysplastic and neoplastic conditions arising from the haematopoietic stem cell or its progeny. Thus the chronic and acute myeloid leukaemias, thrombocythaemia, megakaryocytic myelosis, myelofibrosis, the myelodysplastic syndromes and some cases of aplastic anaemia may be viewed as variants of a single disease process. This view is useful in explaining the common occurrence of mixed forms of disease or interconversions between the myeloproliferative diseases. This variability is a consequence of the development of all the haematopoietic lineages from a single class of haematopoietic stem cell by progressive differentiation. The aetiology of the myeloproliferative diseases in the domestic animals is uncertain but feline leukaemia virus infection has been implicated in the cat. These conditions may be classified as aplastic anaemia, as preleukaemic dysplastic conditions with variable cytopenias and morphological abnormalities of blood cells, as smouldering leukaemias, or as leukaemias with a frankly leukaemic blood or bone marrow.

Animals↗
PubMed2003

Detection and classification of neurotoxins using a novel short-term plasticity quantification method.

A tissue-based biosensor is described for screening chemical compounds that rapidly affect the nervous system. The proposed sensor is an extension of a previous work on cultured hippocampal slices [Biosens. Bioelectron. 16 (2001) 491]. The detection of the chemical compounds is based on a novel quantification method of short-term plasticity (STP) of the CA1 system in acute hippocampal slices, using random electrical impulse sequences as inputs and population spike (PS) amplitudes as outputs. STP is quantified by the first and the second order kernels using a variant of the Volterra modeling approach. This approach is more specific and time-efficient than the conventional paired pulse and fixed frequency train methods [J. Neurosci. Methods 2 (2002) 111]. Describing the functional state of the biosensor, the kernels changed accordingly as chemical compounds were added. The second order kernel was decomposed into nine Laguerre functions. The corresponding Laguerre coefficients along with the first order kernel were used as features for classification purposes. The biosensor was tested using picrotoxin (100 microM), trimethylopropane phosphate (10 microM), tetraethylammonium (4 mM), valproate (5 mM), carbachol (5 mM), DAP5 (25 microM), CNQX (3 microM), and DNQX (0.15, 1.5, 3, 5 and 10 microM). Each chemical compound gave a different feature profile corresponding to its pharmacological class. The first order kernel and the Laguerre coefficients formed the input to an artificial neural network (ANN) comprised of a single layer of perceptrons. The ANN was able to classify each tested compound into its respective class.

Action Potentials↗
PubMed1975

Clear cell sarcoma with melanin pigment.

A patient with a clear cell sarcoma of tendons and aponeuroses arising in the left sacral area is reported. The tumor grossly contained two black foci that had pigment with the staining characteristics of melanin on light microscopy. Electron microscopy of these areas showed the pigment to be within melanosomes. This is the second report of a neoplasm diagnosed as clear cell sarcoma in which melanin was demonstrated; the possibility that the tumor represents a soft tissue variant of malignant melanoma is discussed. It is suggested that clear cell sarcoma is a heterogeneous entity, and that a number of different soft tissue neoplasms may present with a clear cell pattern, making diagnosis and classification difficult.

Adult↗
PubMed2005

Two cases of acute myeloid leukemia with t(11;17) associated with varying morphology and immunophenotype: rearrangement of the MLL gene and a region proximal to the RARalpha gene.

This report describes 2 cases of acute myeloid leukemia (AML), which based on the WHO classification would be classified as AML with an 11q23 (MLL) abnormality, but with contrasting morphologic and immunophenotypic profiles. One case had monocytic features (morphologically and immunophenotypically) with a t(11;17)(q23;q21), a previously identified variant translocation in acute promyelocytic leukemia (APL). The second case had morphologic and immunophenotypic features of APL associated with a t(11;17)(q23;q25). In both cases, fluorescence-in-situ hybridization (FISH) analysis demonstrated that the 11q23 breakpoint involved the MLL gene, but RARalpha was not involved in the 17q breakpoints. These cases illustrate the importance of FISH analysis to confirm the presence of a particular recurring rearrangement.

Acute Disease↗
PubMed2000

Documentation of variations in sinonasal anatomy by intraoperative nasal endoscopy.

OBJECTIVES: Functional endoscopic sinus surgery (FESS) requires a thorough understanding of the variability in sinonasal anatomy. Previous reports have relied primarily on anatomic studies of cadaveric specimens or skulls, or on radiographic analysis. Relatively few comparative anatomic data have been accumulated with endoscopic examination of living patients. STUDY DESIGN: Retrospective review of video recordings of 119 consecutive patients undergoing intraoperative nasal endoscopy at the time of sinonasal surgery. METHODS: At the beginning of each surgical procedure, endoscopic examination of the nasal cavities was performed with 0 degrees and 30 degrees telescopes and recorded with a three-chip video camera on 3/4-inch U-matic videotape. These video records were then reviewed with attention to variations in anatomical configuration of different sinonasal structures. RESULTS: Data demonstrating variations in the anatomical configuration of the following structures of the lateral nasal wall are presented. Middle turbinate: typical (63%), concha bullosa (15%), sagittal cleft (6%), laterally displaced (4%), "L" shaped (3%), medially bent (3%), laterally bent (3%), medially displaced (2%), and transverse cleft (0.5%). Uncinate process: typical (85%) and medially rotated (15%). Ethmoid bulla: typical or balloon (45%), sausage-shaped (34%), and flat (21%). Accessory ostium: round (50%), oval (46%), and kidney-shaped (4%). Sphenoid sinus ostium: oval (42%), slit (32%), and round (26%). The classification system for the anatomical categories is illustrated with digitized images. CONCLUSIONS: This study attempts to provide statistical data regarding variations in sinonasal anatomy in living subjects. Familiarity with such anatomy is important in differentiating normal variants from pathological conditions to optimize surgical treatment of sinus disease, while avoiding complications.

Adolescent↗
PubMed1995

Hereditary nondystrophic myotonias and periodic paralyses.

The hereditary disorders of muscle excitability are now recognized to be caused by defects in the genes encoding muscle ion channels. This led to a new classification of this disease group. The pathophysiology of these disorders has been elucidated on the molecular level to an extent that exceeds the understanding of the disease mechanisms of most other neuromuscular diseases. The seemingly minor variants of the symptom of myotonia were found to be caused by the remarkable difference that either chloride or sodium channel function is impaired. Even more surprising, the basic defects for hyper- and hypokalemic periodic paralysis, often clinically very difficult to distinguish, turned out to be in the sodium and calcium channels, respectively; these channels are considered to have very different functions in muscle physiology. Three new types of myotonic disease, that is, myotonia, fluctuans, myotonia permanens and proximal myotonic myopathy were discovered. An explanation has been provided as to why myotonia congenita may be transmitted as a dominant or recessive trait.

Humans↗
PubMed2004

Pharmacogenomics in cardiovascular clinical trials.

Genomics - having quickly emerged as the central discipline in basic science and biomedical research - is poised to take the center stage in clinical medicine as well over the next few decades. Although there is no specific regulatory guideline on the application of pharmacogenetics to drug development, some recommendations are already included in several published guidelines on drug development. The patients more likely to provide the most valuable information on the specific contribution of a given gene or its variant are those who fail to respond to a drug ('therapeutic failures') and those who develop toxicity to the drug. However, before drawing definite conclusions on subgroups following pharmacogenomic analyses, one must be aware of disease classification, data collection, and how much is known about the disease process. It seems reasonable to collect genomic DNA from all patients enrolled in clinical drug trials (along with appropriate consent to permit pharmacogenetic studies) for the purpose of post hoc analyses. One exception to post hoc genomic analysis is when patients with a specific genotype are excluded from randomization into a clinical trial. Physicians will need to understand the concept of genetic variability, its interactions with the environment (e.g. drug-drug or drug-disease interactions), and its implication for patient care.

Biomedical Research↗
PubMedDate not supplied

Surgery of the mixed laryngocele.

The authors first of all consider the classification of laryngoceles, their pathways of spreading, their statistical incidence, etiopathogenesis and their main clinical aspects. Next, they report on the most important surgical techniques proposed to date by the various experts for the three anatomical variants of laryngocele. As regards more particularly the mixed type, which seems to be the most frequent, the authors raise some objections to the classical methods. In fact, the latter do not always allow a satisfactory result to be achieved, and in this connection reference is also made to negative experiences reported by some authors. They go on to suggest, for mixed laryngocele, a new technique of combined exheresis by way of the external lateral approach and laryngofissure. The authors illustrate in detail the method proposed and report the case of a patient suffering from a voluminous bilateral laryngocele of mixed type, on whom they operated by applying the new technique, with very satisfactory results.

Adult↗
PubMed1987

[Clinical patterns in the development of hypochondriac disorders within the framework of different mental illnesses].

The authors have examined 106 patients with hypochondriac states developing in the presence of various mental diseases. The patients are divided into three nosological groups: psychogenic, exogenic-organic, and endogenic. Variants of the hypochondriac syndrome occurring in each group of the disease are described. Characteristics of the time-course of hypochondriac symptomatology and the stages of the formation of hypochondriac disturbances in relation to their classification with one or another nosological group are outlined.

Adult↗
PubMed1993

Neuropathology of human prion diseases (spongiform encephalopathies).

The human prion diseases (spongiform encephalopathies) comprise Creutzfeldt-Jakob disease (CJD), Gerstmann-Sträussler-Scheinker syndrome (GSS), and kuru. Their clinical characteristics are progressive neurological illness with dementia and ataxia as the most prominent signs. The typical neuropathological changes are limited to the central nervous system; they consist of spongiform degeneration, amyloid plaques, astrocytic gliosis, and nerve cell loss. The aetiology of human spongiform encephalopathies remained unclear for many years, until in the 1960s they were finally recognized as transmissible diseases similar to scrapie in sheep. The infectious agent, termed prion to distinguish it from viruses, consists of protein apparently devoid of functional nucleic acid. The finding that mutations of the prion protein gene are associated with heritable human prion disease has led to wide acceptance of the prion hypothesis. Different mutations have been found in prion disease with distinct clinical and pathological features in a great number of families. Clinical and neuropathological changes not typical of any known variant of human prion disease have been shown to be associated with certain mutations of the PrP gene. Further findings on the molecular biology and biochemistry of the prion protein will probably lead to a new classification of prion diseases.

Alzheimer Disease↗
PubMed2006

Oculocerebrocutaneous and encephalocraniocutaneous lipomatosis syndromes: blind men and an elephant or separate syndromes?

The discovery of relevant causative genes has subdued the lumping versus splitting debate with respect to a growing number of syndromes. However, it remains paramount to define unknown genesis syndromes as precisely and appropriately as possible in order to provide accurate prognosis and to facilitate future research. The presentation of a 14-month-old girl, of normal intelligence, who had a colobomatous right eye with cyst, minor intracranial MRI variants, and an area of sparse scalp hair containing a 1 by 1.5 cm, soft, domed, and indented skin lesion suggested a diagnosis of mild oculocerebrocutaneous syndrome (OCCS). An initial exploration of the literature exposed the extreme variability in cases that have been reported as OCCS, and emphasized its possible relationship to encephalocraniocutaneous lipomatosis (ECCL), thus challenging the initial diagnosis. Cases reported, or discussed by others, as possible OCCS (40) and ECCL (44) were reviewed as completely as possible in an effort to determine whether diagnostic criteria could be developed for these syndromes, and to see whether or not evidence favored their continued separation as two syndromes. The approach used was to summarize the data for all cases, to select major and minor diagnostic criteria on the basis of the relative specificity and/or frequency of a sign, to then apply the criteria in a standard fashion and to review the outcome to see if the classification of cases made clinical sense, and to make appropriate adjustments. The criteria were not chosen so as to separate the syndromes and in some instances the same criteria could apply to either syndrome. An approach is outlined for handling reports of patients that purport to be variants or to expand the spectrum of a syndrome, and in the case of OCCS and ECCL this resulted in most such examples being excluded. Application of diagnostic criteria suggests that OCCS and ECCL are distinct, and that some case reports, including some purporting to expand the spectrum of OCCS, should be excluded, at least until such time as the etiology of these conditions is known and those cases can be tested. These diagnostic criteria were developed on the basis of literature reports that varied in their quantity and quality of detail. Furthermore, in many cases reliance had to be placed on copies of original studies with resultant degradation of photographic information. Modern ocular imaging, and histopathology of eye and skin malformations, will often clarify the specific nature of a malformation and, therefore, define exact diagnostic criteria and leave fewer uncertain cases. In the absence of anomalies in those systems, or if histopathology or appropriate imaging is unavailable, the diagnosis in some cases will continue to remain uncertain; this is not an argument for lumping the syndromes.

Abnormalities, Multiple↗
PubMed2003

Pharmacogenomics of alcohol response and addiction.

Alcoholism is a complex psychiatric disorder that has high heritability (50-60%) and is relatively common; in the US the lifetime prevalence of alcohol dependence is 20% in men and 8% in women. Current psychosocial and pharmacological therapies have relatively modest effects. Treatment is complicated by the fact that alcoholism is often co-morbid with other disorders, including anxiety, depression, and antisocial personality disorder. Approximately 80% of alcoholics smoke cigarettes and there is considerable genetic overlap between nicotine and alcohol addiction. Convergent evidence supports the classification of alcoholics into two broad categories: type 1 - later onset with feelings of anxiety, guilt, and high harm avoidance; and type 2 - early age of onset, usually men, impulsive, antisocial, and with low levels of brain serotonin. The pharmacogenomics of alcohol response is well established; genetic variants for the principal enzymes of alcohol metabolism influence drinking behavior and protect against alcoholism. Vulnerability to alcoholism is likely to be due to multiple interacting genetic loci of small to modest effects. First-line therapeutic targets for alcoholism are neurotransmitter pathway genes implicated in alcohol use. Of particular interest are the 'reward pathway' (serotonin, dopamine, GABA, glutamate, and beta endorphin) and the behavioral stress response system (corticotrophin-releasing factor and neuropeptide Y). Common functional polymorphisms in these genes are likely to be predictive (although each with small effect) of individualized pharmacological responses. Genetic studies, including case-control association studies and genome wide linkage studies, have identified associations between alcoholism and common functional polymorphisms in several candidate genes. Meanwhile, the current pharmacological therapies for alcoholism are effective in some alcoholics but not all. Some progress has been made in elucidating the pharmacogenomic responses to these drugs, particularly in the context of the type 1/type 2 classification system for alcoholics.

Alcohol Drinking↗