Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

A cSNP map and database for human chromosome 21.

S Deutsch1, C Iseli, P Bucher

  • 1Division of Medical Genetics, University of Geneva Medical School, Geneva, Switzerland.

Genome Research
|February 7, 2001
PubMed
Summary

We developed a database of human chromosome 21 (HC21) coding single nucleotide polymorphisms (SNPs) to aid in studying complex genetic diseases. This resource maps 377 SNPs, facilitating research into conditions like bipolar disorder and Down syndrome.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Supraglottic Airway Device to Improve Ventilation Success and Reduce Pulmonary Aspiration during Cardio-Pulmonary Resuscitation by Basic Life Support Rescuers: A Randomized Cross-over Human Cadaver Study.

Prehospital emergency care·2022
Same author

A Preliminary Study of the Fluid Mechanics of Liquid Penetrant Testing.

Journal of research of the National Bureau of Standards (1977)·2021
Same author

Chromatin three-dimensional interactions mediate genetic effects on gene expression.

Science (New York, N.Y.)·2019
Same author

ARMC5 is not implicated in familial hyperaldosteronism type II (FH-II).

Journal of human hypertension·2017
Same author

A four-gene LincRNA expression signature predicts risk in multiple cohorts of acute myeloid leukemia patients.

Leukemia·2017
Same author

Differential effects on gene transcription and hematopoietic differentiation correlate with GATA2 mutant disease phenotypes.

Leukemia·2017

Area of Science:

  • Genomics
  • Human Genetics
  • Bioinformatics

Background:

  • Complex genetic diseases are influenced by variations like single nucleotide polymorphisms (SNPs).
  • Human chromosome 21 (HC21) has a completed genomic sequence with 225 annotated genes.
  • Efficient identification and mapping of potential coding SNPs (cSNPs) are crucial for genetic studies.

Purpose of the Study:

  • To create a comprehensive database and map of coding SNPs (cSNPs) for human chromosome 21 (HC21).
  • To provide a valuable resource for investigating the genetic basis of complex diseases linked to HC21.
  • To establish a validated bioinformatics approach for cSNP discovery.

Main Methods:

  • Generated candidate cSNPs by aligning HC21 genomic sequence to ESTs and mRNAs using a novel SNP identification program.

Related Experiment Videos

  • Employed multiple alignment of known HC21 genes against other human database entries.
  • Conducted gene-targeted cSNP discovery.
  • Developed a novel program for context-dependent SNP identification to differentiate true variations from sequencing errors or paralogous alignments.

    • Main Results:

    • Identified 377 cSNPs on HC21, averaging approximately 1 SNP per 1.5 kb of transcribed sequence.
    • The identified cSNPs cover 65% of the known genes on the chromosome.
    • Bioinformatics approach demonstrated a 78% confirmation rate for predicted cSNPs, with 32% confirmed overall.
    • Established the first chromosome-specific cSNP map for HC21.

    Conclusions:

    • The HC21 cSNP database and map represent a significant resource for genetic research.
    • These SNPs can be utilized to explore the contribution of HC21 loci to complex diseases such as bipolar affective disorder.
    • The findings enable the study of allele-specific contributions to phenotypes associated with Down syndrome.