Genomic Sequence Data: Answers to My Questions

In summary, the conversation discusses the possibility of receiving data about an individual's genome sequence and how to determine if alleles from the same chromosome come from the same parent. It is mentioned that standard whole genome sequencing methods do not allow for this determination and specialized techniques are needed.
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alexepascual
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I wonder. If I received the data (I don't know in what format) of all or part of my genome sequence, whould all the genes and SNP's that are physically in the same chromosome (not its homologous one) show together in the data or the process of sequencing and assembly mixes them up? I understand DNA is chopped in small pieces to do the sequencing. That's why I wonder if there is a way to make sure that all the small pieces that came form one of the two homologuous chromosomes (form the father or the mother) stay together. For example if two genetic variants (I mean of two different genes) show in the same chromosome, can I be sure these two came both from the same parent? I have not received yet any data, but my wife got a small set of SNP's with the intent to get some info about her ancestry. Looking at the raw data, I see that they show the SNP's from the homologous chromosomes as Allele 1 and Allele 2, and all the allele 1's are in the first column and the allele 2's are in the second column. So my question also applies to that situation. I wonder if all the allele 1's form a particular chormosome number come from the same parent or not necessarily. I would guess that maybe in that case, if we are looking at isolated SNP's it may be very hard to know which of the two chormosomes a particular allele came from. If you know about this I'll appreciate your answer.
 
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Determining which alleles are linked to the same chromosome is a process called haplotyping. Standard whole genome sequencing methods do not allow one to determine the haplotype of an individual. Specialized techniques, such as phased sequencing using longer read lengths and higher coverage, are required to determine one's haplotype.
 
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1. What is genomic sequence data?

Genomic sequence data is a set of genetic information that is obtained through the sequencing of an organism's DNA or RNA. It contains the sequence of nucleotides that make up an organism's genetic code.

2. How is genomic sequence data used in scientific research?

Genomic sequence data is used to study the genetic makeup of an organism, including its genes, variations, and mutations. It can also be used to understand the functions of specific genes, identify disease-causing mutations, and develop treatments and therapies for genetic disorders.

3. What technologies are used to generate genomic sequence data?

There are several technologies used to generate genomic sequence data, including Sanger sequencing, next-generation sequencing, and single-molecule sequencing. Each technology has its own advantages and limitations, which scientists consider when selecting the appropriate method for their research needs.

4. What are the challenges in analyzing genomic sequence data?

One of the main challenges in analyzing genomic sequence data is the massive amount of data that is generated. This requires advanced computational tools and techniques to handle and interpret the data accurately. Additionally, the complexity of the data and the presence of genetic variations and mutations can also pose challenges in data analysis.

5. How is genomic sequence data stored and shared among scientists?

Genomic sequence data is typically stored in databases, such as GenBank and the European Nucleotide Archive, which are publicly accessible. Scientists can also share their data through online platforms and repositories, such as NCBI's Sequence Read Archive and the European Bioinformatics Institute's European Genome-phenome Archive.

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