Segmenting the human genome based on states of neutral genetic divergence

Many studies have demonstrated that divergence levels generated by different mutation types vary and covary across the human genome. To improve our still-incomplete understanding of the mechanistic basis of this phenomenon, we analyze several mutation types simultaneously, anchoring their variation to specific regions of the genome. Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from human–orangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to different divergence states—each uniquely characterized by specific combinations of divergence levels. We then parsed the mutagenic contributions of various biochemical processes associating divergence states with a broad range of genomic landscape features. We find that high divergence states inhabit guanine- and cytosine (GC)-rich, highly recombining subtelomeric regions; low divergence states cover inner parts of autosomes; chromosome X forms its own state with lowest divergence; and a state of elevated microsatellite mutability is interspersed across the genome. These general trends are mirrored in human diversity data from the 1000 Genomes Project, and departures from them highlight the evolutionary history of primate chromosomes. We also find that genes and noncoding functional marks [annotations from the Encyclopedia of DNA Elements (ENCODE)] are concentrated in high divergence states. Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants—including those associated with cancer and other diseases—and to improve computational predictions of noncoding functional elements.Whole-genome sequencing studies have demonstrated that divergence estimates for several mutation types (e.g., nucleotide substitutions, insertions, and deletions) vary substantially across the human genome. This phenomenon has been studied at various genomic scales and evolutionary distances (reviewed in ref. 1), and—whereas initially of interest solely to evolutionary biologists—is now entering the purview of main biomedical research. Specifically, human population (e.g., ref. 2) and cancer (3, 4) genome resequencing projects have revealed that incidences of single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and copy number variants (CNVs) vary across the genome. Divergence estimates for different mutation types also covary across the genome (5, 6)—e.g., substitution rates increase in regions with high indel rates (7)—suggesting that regional variation is an important and general characteristic of mutations.Variation in divergence is often linked to genomic landscape features such as base composition, replication timing, and recombination rates (1). For instance, nucleotide substitution rates are elevated in late-replicating regions because of an accumulation of single-stranded DNA susceptible to endogenous damage (8) and are affected by chromatin structure (9) and recombination as a result of either biased gene conversion (BGC) (10) or the mutagenicity of recombination (2). Moreover, nucleotide substitution rates depend nonlinearly on guanine and cytosine (GC) content (11) and are affected by methylation levels and GC content at cytosine—phosphate—guanine (CpG) sites (12) and by replication timing and distance to telomeres at non-CpG sites (13). Covariation in divergence among rates of different mutation types can also be at least partly attributed to the influence of a common genomic landscape (5). Importantly, we note that, whereas selection may indeed operate in noncoding regions, it is unlikely to explain the large degree of variation and covariation in divergence estimates computed from putatively neutral sequences (1, and references therein). Divergence computed for neutral DNA ought to reflect mutation, BGC, and—for relatively distant species—only a minimal amount of diversity.Anchoring variation and covariation of divergence estimates for different mutation types to specific regions of the genome is crucial for elucidating how biochemical processes—e.g., replication and recombination—drive mutagenesis (8, 10) and for understanding genome evolution. Such a “geographic” characterization may correlate with the spatial distribution of genes; for instance, cellular receptor and housekeeping genes tend to locate, respectively, in high and low nucleotide substitution rate regions (14). It may also aid prediction of noncoding functional elements (15, 16) and studies of the genetic basis of disease. For instance, it could assist in (i) discerning whether a locus exhibits an excess of mutations because it resides in a hotspot, thus preventing false positive associations with a disease; and (ii) identifying loci with mutational signatures typical of a disease, e.g., explaining frequent coincidence in tumors of sites prone to DNA damage and chromosomal instability (17).With this motivation, we used hidden Markov models (HMMs) (18), a well-established statistical tool, to analyze human divergence for different mutation types. An HMM models a sequence of observations as governed by underlying states that are not directly observable (hidden) but can be inferred based on the data. These states alternate along the sequence following a Markovian structure, i.e., the state governing a given observation may depend on the state governing the preceding observation. Maximum likelihood techniques are used to select an appropriate number of states, characterize them, and partition the sequence into contiguous segments governed by each state.In genomics, HMMs have been used to model stretches of DNA—the sequences of observations—in a variety of applications ranging from gene finders (19) to epigenomic segmentations (20, 21). In our study, we compute divergence estimates for four mutation types—substitutions, insertions, deletions, and microsatellite repeat number alterations—in nonoverlapping windows of neutrally evolving sequences present in human–orangutan genomic alignments. Modeling the resulting observations with HMMs, we identify distinct divergence states characterized by biologically meaningful combinations of elevated, average, or depressed divergence levels for the four mutation types, e.g., a state where only microsatellite mutations are elevated, whereas the other divergence types are average; one where substitutions, insertions, and deletions are all elevated, whereas microsatellite divergence is average, etc. Correspondingly, we partition the genome into chromosomal segments governed by these states. Our analysis departs from previous applications in considering several mutation types simultaneously—thus accounting for their interdependencies—and in generating segmentations not on a small 100-bp scale (22), but on a larger 1-Mb scale that robustly captures variation in divergence for mammalian genomes (11, 23). Additionally, we investigate whether divergence states differ in genomic landscape features that proxy underlying mutagenic processes, correlate with the spatial organization of functional elements, and persist when assessed from human diversity estimates or for varying genomic scales.     

Megavoltage radiotherapy using water bolus in the treatment of Kaposi's sarcoma

Between 1976 and 1983, 28 patients with Kaposi's sarcoma were treated in the Department of Radiation and Clinical Oncology of the Hadassah University Hospital in Jerusalem. Most of the patients (16, i.e. 57%) were Jews of European origin. Eighteen (64.2%) of the patients presented with severe leg edema in addition to multifocal, disseminated skin lesions. Only one patient was free of clinical disease in the lower extremities. Large, ulcerated masses were seen in three patients. The affected limbs were immersed in a water bath and irradiated with two-opposing portals to a total dose of 3000 rads. Total disappearance of the skin lesions was achieved in 89% of the patients, although the limb edema regressed completely in only 56% of the patients.     

Key problems of antitumor immunity and glycoconjugates]

Two key problems of the antitumour immunity are considered: 1) very rapid changing of tumour-associated antigens; 2) tumour immunosuppression. Carbohydrate structures of the tumour-associated antigens (mainly glycoconjugates) are changing much more rapidly (hours, days) than the clones of antitumour T-killers proliferate. It is stated that the fundamental question of the nature of the glycoconjugate and endogenous lectin changing is not sufficiently studied. The endogenous lectins of the lymphocyte and macrophage surface are an old recognizing system responsible for a natural cell resistance to the tumour. Stimulation of this system by means of bacterial and syngeneic glycoconjugates is a promising direction in the tumour immunotherapy. Concerning the second aspect, the data are summarized according to which tumour cells produce inhibiting factors, including glycoconjugates, that suppress both proliferation and function of lymphocytes and macrophages. Developing the methods of rehabilitation of the immune system cells with the use of activating glycoconjugates and cytokines is the second important trend in the tumour immunotherapy.     

Electron-beam therapy for mycosis fungoides: the Stanford University experience.

The use of high-dose electron-beam therapy for mycosis fungoides at Stanford University is reviewed. Since 1966, 140 patients have been treated in this fashion. Their clinical characteristics including initial extent of disease are reviewed. The results of routine staging studies are examined. Eighty-four percent of the patients achieved an initial complete remission; this was inversely related to the initial extent of skin involvement. The overall survival rate was 46% at 10 years with the major prognostic factor being the initial extent of skin involvement. Other factors which had an influence on the patient's progrnosis included the presence of palpable adenopathy, the patient's age, the achieving of an initial complete remission, the initial dose of electron-beam therapy, and the treatment with adjuvant topical mechlorethamine. The development of a rationale for the treatment of patients with all stages of mycosis fungoides based upon these clincal observations is discussed.     

Anterior decompression of the spine for metastatic epidural cord compression: A promising avenue of therapy?

Most metastatic epidural tumors arise in a vertebral body and invade the anterior epidural space. Therefore, it is logical to decompress the spine anteriorly and not by traditional laminectomy. Surgical decompression is indicated if relapse occurs after radiotherapy and further radiation cannot be administered, if there is neurological deterioration during radiotherapy, and when histological diagnosis of the primary tumor is lacking. This pilot study consists of eleven consecutive anterior decompressions of the spine performed in nine patients. In seven instances other treatment modalities had been exhausted, and in four patients a tissue diagnosis was lacking. Before operation eight of the patients were nonambulatory, four of them paraplegic. Following decompression all but one patient became ambulatory. At operation the main bulk of the compressing tumor was found anterior or anterolateral to the cord. Spine stabilization was done when stability was a problem. Wound infection in one patient was the only postoperative complication. The encouraging outcome of our management prompts us to suggest that anterior decompression of the spine should be considered more often in metastatic compression of the cord and cauda equina.     

Eruption of rootless teeth in congenital renal disease

Eruption of rootless mandibular premolars and other dental defects in a girl suffering from congenital kidney disease are described. The successful management of these excessively mobile teeth allowed them to develop roots of sufficient length. Hypotheses of tooth emergence are viewed in the light of these rootless eruptions.     

Détermination de constantes d'acidité d'amidines N-N′-substituées. Relations entre les pKA et les vibrations IR — I. Acétamidines et métacrylamidines

Changes in the ultraviolet absorption spectra with pH in aqueous solution were used to determine the pK_A values of amidines. A new mathematical procedure was used to study sparingly soluble compounds. In this technique, all the experimental data are used to solve for the absorbance of the insoluble basic species and for the pK_A value by a ‘complex method’ of optimization, which is more general than the classical least-squares method. A relationship between a double bond vibration frequency and the acidity constants of these compounds has been demonstrated.