Academic Journal
Characterizing Fractal Genetic Variation in the Human Genome from the Hapmap Project
| العنوان: | Characterizing Fractal Genetic Variation in the Human Genome from the Hapmap Project |
|---|---|
| المؤلفون: | Borri, Alessandro, Cerasa, Antonio, Tonin, Paolo, Citrigno, Luigi, Porcaro, Camillo |
| المساهمون: | Borri, Alessandro, Cerasa, Antonio, Tonin, Paolo, Citrigno, Luigi, Porcaro, Camillo |
| سنة النشر: | 2022 |
| المجموعة: | Padua Research Archive (IRIS - Università degli Studi di Padova) |
| مصطلحات موضوعية: | Fractal dimension (FD), HapMap project, Higuchi’s fractal dimension (HFD), box-counting dimension (BCD), genetic variation, human genome, machine learning, Algorithm, Human, Fractal, Genome |
| الوصف: | Over the last decades, the exuberant development of next-generation sequencing has revolutionized gene discovery. These technologies have boosted the mapping of single nucleotide polymorphisms (SNPs) across the human genome, providing a complex universe of heterogeneity characterizing individuals worldwide. Fractal dimension (FD) measures the degree of geometric irregularity, quantifying how "complex" a self-similar natural phenomenon is. We compared two FD algorithms, box-counting dimension (BCD) and Higuchi's fractal dimension (HFD), to characterize genome-wide patterns of SNPs extracted from the HapMap data set, which includes data from 1184 healthy subjects of eleven populations. In addition, we have used cluster and classification analysis to relate the genetic distances within chromosomes based on FD similarities to the geographical distances among the 11 global populations. We found that HFD outperformed BCD at both grand average clusterization analysis by the cophenetic correlation coefficient, in which the closest value to 1 represents the most accurate clustering solution (0.981 for the HFD and 0.956 for the BCD) and classification (79.0% accuracy, 61.7% sensitivity, and 96.4% specificity for the HFD with respect to 69.1% accuracy, 43.2% sensitivity, and 94.9% specificity for the BCD) of the 11 populations present in the HapMap data set. These results support the evidence that HFD is a reliable measure helpful in representing individual variations within all chromosomes and categorizing individuals and global populations. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | info:eu-repo/semantics/altIdentifier/pmid/35579974; info:eu-repo/semantics/altIdentifier/wos/WOS:000800284400002; volume:32; issue:6; firstpage:2250028; journal:INTERNATIONAL JOURNAL OF NEURAL SYSTEMS; http://hdl.handle.net/11577/3455857; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85130463034 |
| DOI: | 10.1142/S0129065722500289 |
| الاتاحة: | http://hdl.handle.net/11577/3455857 https://doi.org/10.1142/S0129065722500289 |
| رقم الانضمام: | edsbas.8ABCB4B5 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1142/S0129065722500289 |
|---|