title: ÐÐ¾Ð¸ÑÐº Ð±Ð¾Ð»ÑÑÐ¸Ñ ÑÑÑÑÐºÑÑÑÐ½ÑÑ Ð²Ð°ÑÐ¸Ð°Ð½ÑÐ¾Ð² Ð¿Ð¾ Ð´Ð°Ð½Ð½ÑÐ¼ Hi-C Ð¸ Ð¾Ð¿ÑÐ¸ÑÐµÑÐºÐ¾Ð³Ð¾ ÐºÐ°ÑÑÐ¸ÑÐ¾Ð²Ð°Ð½Ð¸Ñ Ð³ÐµÐ½Ð¾Ð¼Ð°
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð¼Ð°Ð³Ð¸ÑÑÑÐ°
titleType: Subtitle
title: Detecting large structural variants using Hi-C data and optical genome mapping
Creators: name: ÐÑÐµÐ², ÐÐ°Ð»ÐµÑÐ¸Ð¹
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2024
Subjects: ÑÑÑÑÐºÑÑÑÐ½ÑÐµ Ð²Ð°ÑÐ¸Ð°Ð½ÑÑ
ÐºÐ¾Ð½ÑÐ°ÐºÑÑ Ñ ÑÐ¾Ð¼Ð°ÑÐ¸Ð½Ð°
Ð¾Ð¿ÑÐ¸ÑÐµÑÐºÐ¸Ðµ ÐºÐ°ÑÑÑ Ð³ÐµÐ½Ð¾Ð¼Ð°
structural variants
chromatin contacts
optical genome maps

description: Ð ÑÐ°Ð±Ð¾ÑÐµ Ð¾Ð¿Ð¸ÑÑÐ²Ð°ÑÑÑÑ ÑÐ¿Ð¾ÑÐ¾Ð±Ñ Ð¿Ð¾Ð¸ÑÐºÐ° ÑÑÑÑÐºÑÑÑÐ½ÑÑ Ð²Ð°ÑÐ¸Ð°Ð½ÑÐ¾Ð² Ð² Ð³ÐµÐ½Ð¾- Ð¼Ðµ. Ð Ð°Ð·ÑÐ°Ð±Ð¾ÑÐ°Ð½Ð° Ð¼Ð¾Ð´Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ñ ÑÑÑÐµÑÑÐ²ÑÑÑÐµÐ³Ð¾ Ð¼ÐµÑÐ¾Ð´Ð° Ð¿Ð¾Ð¸ÑÐºÐ° ÑÑÑÑÐºÑÑÑÐ½ÑÑ Ð²Ð°ÑÐ¸Ð°Ð½ÑÐ¾Ð² Ð¿Ð¾ ÐºÐ°ÑÑÐ°Ð¼ ÑÐ°ÑÑÐ¾Ñ Ð¿Ð¾Ð¿Ð°ÑÐ½ÑÑ ÐºÐ¾Ð½ÑÐ°ÐºÑÐ¾Ð² Ð¼ÐµÐ¶Ð´Ñ ÑÑÐ°ÑÑÐºÐ°Ð¼Ð¸ ÑÑÐ¾Ð¼Ð°ÑÐ¸Ð½Ð°, Ð¿Ð¾Ð»ÑÑÐµÐ½Ð½ÑÑ Ñ Ð¿Ð¾Ð¼Ð¾ÑÑÑ ÑÐµÑÐ½Ð¾Ð»Ð¾Ð³Ð¸Ð¸ Hi-C. ÐÑÐµÐ´Ð»Ð¾Ð¶ÐµÐ½Ð½Ð°Ñ Ð¼Ð¾Ð´Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ñ ÑÑÑÐµÑÑÐ²ÑÑÑÐµÐ³Ð¾ Ð°Ð»Ð³Ð¾ÑÐ¸ÑÐ¼Ð° Ð¸ÑÐ¿Ð¾Ð»ÑÐ·ÑÐµÑ, Ð¿Ð¾Ð¼Ð¸Ð¼Ð¾ ÐºÐ°ÑÑ Hi-C, Ð´Ð°Ð½Ð½ÑÐµ Ð¾ Ð½Ð°Ð»Ð¸ÑÐ¸Ð¸ Ð¼Ð¾Ð´Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¹ Ð³Ð¸ÑÑÐ¾Ð½Ð¾Ð² Ð²Ð´Ð¾Ð»Ñ Ð³ÐµÐ½Ð¾Ð¼Ð° (Ð¿ÑÐ¾ÑÐ¸Ð»Ð¸ ChIP-Seq): Ð½Ð°Ð¹Ð´ÐµÐ½Ð½ÑÐµ Ð¿Ð¾ ÐºÐ°ÑÑÐ°Ð¼ ÐºÐ¾Ð½ÑÐ°ÐºÑÐ¾Ð² Ð²Ð¾Ð·Ð¼Ð¾Ð¶Ð½ÑÐµ ÑÑÑÑÐºÑÑÑÐ½ÑÐµ Ð²Ð°ÑÐ¸Ð°Ð½ÑÑ Ð´Ð¾Ð¿Ð¾Ð»Ð½Ð¸ÑÐµÐ»ÑÐ½Ð¾ Ð¿ÑÐ¾ÑÐ¾Ð´ÑÑ ÑÐ¸Ð»ÑÑÑÐ°ÑÐ¸Ñ, ÐºÐ¾ÑÐ¾ÑÐ°Ñ Ð¾Ð¿Ð¸ÑÐ°ÐµÑÑÑ Ð½Ð° Ð¿ÑÐ¸Ð·Ð½Ð°ÐºÐ¸, Ð¿Ð¾Ð»ÑÑÐµÐ½Ð½ÑÐµ Ð¸Ð· Ð´Ð°Ð½Ð½ÑÑ ChIP-Seq. ÐÐ° Ð¿ÑÐ¸Ð¼ÐµÑÐµ ÐºÐ»ÐµÑÐ¾ÑÐ½Ð¾Ð¹ Ð»Ð¸Ð½Ð¸Ð¸ U2OS Ð±ÑÐ»Ð¾ Ð¿Ð¾ÐºÐ°Ð·Ð°Ð½Ð¾, ÑÑÐ¾ ÑÑÐ¾Ñ Ð¼ÐµÑÐ¾Ð´ Ð¾Ð±Ð»Ð°Ð´Ð°ÐµÑ Ð¿Ð¾Ð²ÑÑÐµÐ½Ð½Ð¾Ð¹ ÑÐ¿ÐµÑÐ¸ÑÐ¸ÑÐ½Ð¾ÑÑÑÑ Ð¿Ð¾ ÑÑÐ°Ð²Ð½ÐµÐ½Ð¸Ñ Ñ Ð±Ð°Ð·Ð¾Ð²ÑÐ¼ Ð°Ð»Ð³Ð¾ÑÐ¸ÑÐ¼Ð¾Ð¼, ÑÐ¾ ÐµÑÑÑ Ð»ÑÑÑÐµ Ð¾ÑÐ»Ð¸ÑÐ°ÐµÑ Ð¸ÑÑÐ¸Ð½Ð½ÑÐµ ÑÑÑÑÐºÑÑÑÐ½ÑÐµ Ð²Ð°ÑÐ¸Ð°Ð½ÑÑ Ð¾Ñ Ð¿ÑÐ¾ÑÐ¸Ñ Ð°Ð½Ð¾Ð¼Ð°Ð»Ð¸Ð¹ Ð½Ð° ÐºÐ°ÑÑÐ°Ñ ÐºÐ¾Ð½ÑÐ°ÐºÑÐ¾Ð². Ð¢Ð°ÐºÐ¶Ðµ Ð¿ÑÐµÐ´ÑÑÐ°Ð²Ð»ÐµÐ½ Ð¼ÐµÑÐ¾Ð´ Ð¾Ð±Ð½Ð°ÑÑÐ¶ÐµÐ½Ð¸Ñ ÑÑÑÑÐºÑÑÑÐ½ÑÑ Ð²Ð°ÑÐ¸Ð°Ð½ÑÐ¾Ð² Ñ Ð¿Ð¾Ð¼Ð¾ÑÑÑ Ð¾Ð¿ÑÐ¸ÑÐµÑÐºÐ¾Ð³Ð¾ ÐºÐ°ÑÑÐ¸ÑÐ¾Ð²Ð°Ð½Ð¸Ñ Ð³ÐµÐ½Ð¾Ð¼Ð°. Ð¦ÐµÐ½ÑÑÐ°Ð»ÑÐ½ÑÐ¹ ÑÐ»ÐµÐ¼ÐµÐ½Ñ Ð¼ÐµÑÐ¾Ð´Ð° â Ð¼Ð¾Ð´ÐµÐ»Ñ Ð¼Ð°ÑÐ¸Ð½Ð½Ð¾Ð³Ð¾ Ð¾Ð±ÑÑÐµÐ½Ð¸Ñ Ð´Ð»Ñ Ð¿Ð¾Ð¸ÑÐºÐ° ÑÐ¾Ð¾ÑÐ²ÐµÑÑÑÐ²Ð¸Ñ Ð¸Ð·Ð¾Ð±ÑÐ°Ð¶ÐµÐ½Ð¸Ñ Ð¼Ð¾Ð»ÐµÐºÑÐ»Ñ ÐÐÐ Ñ ÑÐ»ÑÐ¾ÑÐµÑÑÐµÐ½ÑÐ½ÑÐ¼Ð¸ Ð¼ÐµÑÐºÐ°Ð¼Ð¸, Ð¿Ð¾Ð»ÑÑÐµÐ½Ð½Ð¾Ð³Ð¾ Ð¾Ð¿ÑÐ¸ÑÐµÑÐºÐ¸Ð¼ ÑÐºÐ°Ð½ÐµÑÐ¾Ð¼, Ð¸ ÑÐµÑÐµÑÐµÐ½ÑÐ½Ð¾Ð¹ Ð¿Ð¾ÑÐ»ÐµÐ´Ð¾Ð²Ð°ÑÐµÐ»ÑÐ½Ð¾ÑÑÐ¸. Ð ÑÐ°Ð±Ð¾ÑÐµ Ð±ÑÐ»Ð° Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°Ð½Ð° Ð¼Ð¾Ð´Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ñ Ð¼Ð¾Ð´ÐµÐ»Ð¸ Ð¼Ð°ÑÐ¸Ð½Ð½Ð¾Ð³Ð¾ Ð¾Ð±ÑÑÐµÐ½Ð¸Ñ, Ð¾ÑÐ½Ð¾Ð²Ð°Ð½Ð½Ð¾Ð¹ Ð½Ð° Ð´Ð²ÑÑ Ð½ÐµÐ¹ÑÐ¾ÑÐµÑÑÑ-ÑÐ½ÐºÐ¾Ð´ÐµÑÐ°Ñ, Ð¿ÑÐ¾ÐµÑÐ¸ÑÑÑÑÐ¸Ñ ÑÑÐ°Ð³Ð¼ÐµÐ½ÑÑ ÑÐµÑÐµÑÐµÐ½ÑÐ½Ð¾Ð¹ Ð¿Ð¾ÑÐ»ÐµÐ´Ð¾Ð²Ð°ÑÐµÐ»ÑÐ½Ð¾ÑÑÐ¸ Ð¸ Ð¸Ð·Ð¾Ð±ÑÐ°Ð¶ÐµÐ½Ð¸Ñ Ð¼Ð¾Ð»ÐµÐºÑÐ» Ð² Ð¾Ð±ÑÐµÐµ ÑÐºÑÑÑÐ¾Ðµ Ð¿ÑÐ¾ÑÑÑÐ°Ð½ÑÑÐ²Ð¾. ÐÐ¾Ð´Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ñ Ð¿Ð¾Ð·Ð²Ð¾Ð»Ð¸Ð»Ð° ÑÐ»ÑÑÑÐ¸ÑÑ ÑÐ¾ÑÐ½Ð¾ÑÑÑ Ð²ÑÑÐ°Ð²Ð½Ð¸Ð²Ð°Ð½Ð¸Ñ Ð¸, ÐºÐ°Ðº ÑÐ»ÐµÐ´ÑÑÐ²Ð¸Ðµ, Ð¿Ð¾Ð²ÑÑÐ¸ÑÑ ÐºÐ°ÑÐµÑÑÐ²Ð¾ Ð¿Ð¾Ð¸ÑÐºÐ° ÑÑÑÑÐºÑÑÑÐ½ÑÑ Ð²Ð°ÑÐ¸Ð°Ð½ÑÐ¾Ð² ÐºÐ»ÐµÑÐ¾ÑÐ½Ð¾Ð¹ Ð»Ð¸Ð½Ð¸Ð¸ U2OS.
description: The paper describes methods for searching for structural variants in the genome. A modification of the existing method for searching for structural variants using frequency maps of pairwise contacts between chromatin regions obtained using Hi-C technology has been developed. The proposed modification of the existing algorithm uses, in addition to Hi-C maps, data on the presence of histone modifications along the genome (ChIP-Seq profiles): possible structural variants found from contact maps are additionally filtered, which is based on features obtained from ChIP-Seq data. Using the U2OS cell line as an example, it was shown that this method has increased specificity compared to the basic algorithm, that is, it better distinguishes true structural variants from other anomalies in contact maps. A method for detecting structural variants using optical genome mapping is also presented. The central element of the method is a machine learning model for searching for a match between an image of a DNA molecule with fluorescent tags obtained by an optical scanner and a reference sequence. The work used a modification of a machine learning model based on two encoder neural networks that project fragments of the reference sequence and images of molecules into a common latent space. The modification made it possible to improve the accuracy of the alignment and, as a result, improve the quality of the search for structural variants of the U2OS cell line.