Search results for "INDEL"

Calreticulin Mutations in Myeloproliferative Neoplasms: Comparison of Three Diagnostic Methods

2015

International audience; Calreticulin (CALR) mutations have recently been reported in 70-84% of JAK2V617F-negative myeloproliferative neoplasms (MPN), and this detection has become necessary to improve the diagnosis of MPN. In a large single-centre cohort of 298 patients suffering from Essential Thrombocythemia (ET), the JAK2V617F, CALR and MPL mutations were noted in 179 (60%), 56 (18.5%) and 13 (4.5%) respectively. For the detection of the CALR mutations, three methods were compared in parallel: high-resolution melting-curve analysis (HRM), product-sizing analysis and Sanger sequencing. The sensitivity for the HRM, product-sizing analysis and Sanger sequencing was 96.4%, 98.2% and 89.3% re…

Free sequences and the tightness of pseudoradial spaces

2019

Let F(X) be the supremum of cardinalities of free sequences in X. We prove that the radial character of every Lindelof Hausdorff almost radial space X and the set-tightness of every Lindelof Hausdorff space are always bounded above by F(X). We then improve a result of Dow, Juhasz, Soukup, Szentmiklossy and Weiss by proving that if X is a Lindelof Hausdorff space, and $$X_\delta $$ denotes the $$G_\delta $$ topology on X then $$t(X_\delta ) \le 2^{t(X)}$$ . Finally, we exploit this to prove that if X is a Lindelof Hausdorff pseudoradial space then $$F(X_\delta ) \le 2^{F(X)}$$ .

Cardinal estimates involving the weak Lindelöf game

2021

AbstractWe show that if X is a first-countable Urysohn space where player II has a winning strategy in the game $$G^{\omega _1}_1({\mathcal {O}}, {\mathcal {O}}_D)$$ G 1 ω 1 ( O , O D ) (the weak Lindelöf game of length $$\omega _1$$ ω 1 ) then X has cardinality at most continuum. This may be considered a partial answer to an old question of Bell, Ginsburg and Woods. It is also the best result of this kind since there are Hausdorff first-countable spaces of arbitrarily large cardinality where player II has a winning strategy even in the weak Lindelöf game of countable length. We also tackle the problem of finding a bound on the cardinality of a first-countable space where player II has a wi…

Generalized Weyl's theorem and quasi-affinity

2010

An Integral Version of Ćirić’s Fixed Point Theorem

2011

We establish a new fixed point theorem for mappings satisfying a general contractive condition of integral type. The presented theorem generalizes the well known Ciric's fixed point theorem [Lj. B. Ciric, Generalized contractions and fixed point theorems, Publ. Inst. Math. 12 (26) (1971) 19-26]. Some examples and applications are given.

Increasing chains and discrete reflection of cardinality

2013

Combining ideas from two of our previous papers, we refine Arhangel'skii Theorem by proving a cardinal inequality of which this is a special case: any increasing union of strongly discretely Lindelof spaces with countable free sequences and countable pseudocharacter has cardinality at most continuum. We then give a partial positive answer to a problem of Alan Dow on reflection of cardinality by closures of discrete sets.

Infinite games and cardinal properties of topological spaces

2015

Inspired by work of Scheepers and Tall, we use properties defined by topological games to provide bounds for the cardinality of topological spaces. We obtain a partial answer to an old question of Bell, Ginsburg and Woods regarding the cardinality of weakly Lindel¨of first-countable regular spaces and answer a question recently asked by Babinkostova, Pansera and Scheepers. In the second part of the paper we study a game-theoretic version of cellularity, a special case of which has been introduced by Aurichi. We obtain a game-theoretic proof of Shapirovskii’s bound for the number of regular open sets in an (almost) regular space and give a partial answer to a natural question about the produ…

Cardinal invariants of cellular Lindelof spaces

2018

A space X is said to be cellular-Lindelof if for every cellular family $$\mathcal {U}$$ there is a Lindelof subspace L of X which meets every element of $$\mathcal {U}$$ . Cellular-Lindelof spaces generalize both Lindelof spaces and spaces with the countable chain condition. Solving questions of Xuan and Song, we prove that every cellular-Lindelof monotonically normal space is Lindelof and that every cellular-Lindelof space with a regular $$G_\delta $$ -diagonal has cardinality at most $$2^\mathfrak {c}$$ . We also prove that every normal cellular-Lindelof first-countable space has cardinality at most continuum under $$2^{<\mathfrak {c}}=\mathfrak {c}$$ and that every normal cellular-Lindel…

Variable-order reference-free variant discovery with the Burrows-Wheeler Transform

2020

Abstract Background In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly improves sensitivity and precision of previous de Bruijn graphs based tools by overcoming several of their limitations, namely: (i) the need to establish a fixed value, usually small, for the order k, (ii) the loss of important information such as k-mer coverage and adjacency of k-mers within the same read, and (iii) bad performance in repeated regions longer than k bases. The preliminary tool, however, was able to identify only SNPs and it was too slow and memory con…

No evidence of EMAST in whole genome sequencing data from 248 colorectal cancers.

2021

Microsatellite instability (MSI) is caused by defective DNA mismatch repair (MMR), and manifests as accumulation of small insertions and deletions (indels) in short tandem repeats of the genome. Another form of repeat instability, elevated microsatellite alterations at selected tetranucleotide repeats (EMAST), has been suggested to occur in 50% to 60% of colorectal cancer (CRC), of which approximately one quarter are accounted for by MSI. Unlike for MSI, the criteria for defining EMAST is not consensual. EMAST CRCs have been suggested to form a distinct subset of CRCs that has been linked to a higher tumor stage, chronic inflammation, and poor prognosis. EMAST CRCs not exhibiting MSI have b…