Questions related to Human Genetics
Is it somehow possible to improve human personality through genetics? Dengue fever treatment with the help of gene mutation. The help of genetic tests in a fight against Brain and heart diseases.
I have 3 Illumina paired-end sequencing data of humans. I want to assemble these 3 genomes. My final goal is to retrieve some gene sequences from these 3 genomes.
1) Please suggest to me any pipelines or papers that can help to assemble these genomes.
2) Can I retrieve some specific gene sequence from these assembled genomes? If yes, please suggest me a way to do it.
3) If no, Is there any other alternative??
A big thank you in advance...
I have genotyped my lines using Infinium 6k SNIP CHIP and have received variants in hapmap format. I want to convert this into VCF format so that i can annotate variants using some online tools.
I have a few human protein-coding gene's DNA sequences (nearly 50kb nt length) and I want to get, only coding sequences from them. Is there any method available to do so??
If yes please suggest me some.
A big thank you in advance.
I have human WGS raw reads and paired-end data. Illumina Hi-Seq 2000 was used for sequencing.
I want to assemble this genome either de-novo or reference-based. I want to assemble it chromosome-specifically so I can only focus on my chromosome of interest. That will save a lot of time for me. And my other goal is to extract a specific gene sequence for it.
1. Please recommend any standard pipelines or literature to me.
2. Can I extract a specific gene or protein sequence from it? If yes, please suggest me the methods for that too.
A big thank you in advance. :)
Is there a way to find repressor/inhibition factor for a gene? Is there a website that list them? I found it to be much harder to find compare to transcription factors...
Have you investigated publications associated with COVID-19 host risk factors and immunopathogenesis related research?
We are all aware that SARS-CoV-2 infection and disease risk factors are complex, resulting in widely varying outcomes, ranging from asymptomatic to severe illness, and death. To be able to evaluate one's own risk related to COVID-19, multiple contributing factors must be considered, including the well known and frequently discussed risk factors of old age, obesity, diabetes, social circumstances, environmental circumstances, and other commonly described co-morbidities along with SARS-CoV-2 variant behaviors. However, the well known and openly discussed risk factors are insufficient to explain the widely varying outcomes of SARS-CoV-2 exposure. Therefore, in the commonly used public domain information sources, some information is missing concerning additional, lesser discussed, but potentially critically important risk factors. It is clear to me that there is no single factor that can determine any particular individual's risk, therefore more information is needed to aid in risk assessment. In no way is this information outcome deterministic, and only represents additional statistical factors to consider when assessing one's own risk to exposure to SARS-CoV-2.
Well, I recently started looking into some of this research, and I would like to share some research that I think could be very important, and ultimately shed some more light on COVID-19, human host immunopathogenesis, and risk. Some of these papers summarize and evaluate research, performed by others, on various host factors that may be additional indicators of SARS-CoV-2 infection and associated disease severity risk. I have included links to articles, preprints, and studies so that we all can be aware of established and up and coming research. All of these articles are open and freely available to the public. I have also included a link to the Wikipedia website on global blood type distribution as a general reference. Do you know your blood type?
I am providing this information to you in the role of a Pure Scientist as described by Rojer A Pielke Jr. in his book titled "The Honest Broker: Making Sense of Science in Policy and Politics." I let you interpret the information and decide on its importance and relevance.
Please feel free to comment on this research.
Allan Haas, PhD
Article Mapping the human genetic architecture of COVID-19, https://www.nature.com/articles/s41586-021-03767-x
Study COVID-19 Genetics Publications https://www.covid19hg.org/results/r6/
Pielke Jr, R.A., 2007. The honest broker: making sense of science in policy and politics. Cambridge University Press.
I tried amplifying the CGG at 5'UTR of the FMRP1 gene by TP-PCR but it was not successful. I ended up with no amplification but when I used the primers flanking this repeat (short PCR) it worked with accuprime GC rich taq pol. So any suggestions from experts who have worked on this gene?
In Europe (in France and Germany at least), there is a new cultural-political position suggesting there were no human races … Not really … only as a delusion… as a constructed deception originating from the early modern times of beginning colonialism. – So not whites, no blacks (in former times: “negros” – sorry, I apologize for this), no yellow or Mongolian race, no Eskimos and so on.
The traditionalists in Europe still oppose this position and complain about a new ideological war with the progressive activists, who try for instance to make jobs dependent on compliance to the no-race-concept.
I would be especially interested in the opinions of coloured people and of non-Westerners. (But this is not meant as an exclusion … So all are invited (independent of any external traits) …).
If you are well-experienced in one of the fields Complex Networks, Human Genetics, or Statistical Mechanics and would like to collaborate with us in our project please contact me at:
Project title: Statistical Mechanics of Human Genes Interactions
Hi, I would like to start a conversation concerning genetic testing. What do you think what the advantages and disadvantages of genetic testing from the point of citizen’s and country’s view are? I would be glad for any texts and responses :) Thanks in advance!
Copy number variations (CNVs) are the gains or losses of genomic regions which range from 500 bases upwards in size. Whole-genome studies have revealed the presence of large numbers of CNV regions in human and a broad range of genetic diversity among the general population. CNVs have been the focus of many recent studies because of their roles in human genetic disorders.
We all know that human genome have 20000 plus genes. That's we know through structural annotations. But I like to have an estimate how many gene among them have clear known assigned function. Please provide any link or paper where I can find this information.
As many studies identified of genetic variants linked to training responses and sport-related traits, we could hypothesize that the R allele was more common in sprint and power athletes and the X allele more common in endurance athletes. Other said, the Middle/Long distance runner (X allele) was would have less response to strength training and Sprinter (R allele) would have less response to endurance training. However, in fact Sprinter would need endurance training to improve aerobic capacity and specific endurance and MD/LD need strength training as well.
Due to the fact, that there are huge amounts of drops outs in athletes career for talented youth Sprinter/MD/LD runners, therefore have a couple of questions :
1. Is any biomarkers we could use to get proper limit of load (Intensity, reps, and recovery) for Sprinter (R allele) while doing endurance exercise or for MD/LD runners (X allele) while performing strength/speed training, so they can keep their genetic potential ?
2. How we could know the proper limit of load/intensity for strength, speed training for MD/LD runners or endurance training for sprinters ?
3. Is the quality of R allele (i.g. speed of muscle contraction) or X (i.g. O2 consumption) allele will reduce due to mismatched training ?
Thank in advance.
What is the relationship between the population's genetic and geographic distance?
I appreciate your help.
I want to learn how I can split the x-axis in which chromosomes are represented in segments with unequal lengths. In the y axis p-values of average ranks are represented.
As there is very little data available for CEP126 gene on databases, i would like to know if there is anybody or any lab working on this gene.
I want to study the inference of the admixed population into different ancestries but I can't understand why it's important to consider the background linkage disequilibrium (LD) between markers.
I appreciate your help.
Our lab just obtained some 5XFAD Het mice that we plan to use. Our plan is to use WT, Hets, and Homozygous animals and was wondering if anyone had a better way to genotype them besides using real-time PCR (which is really expensive). Anyone has any primers suggestions that we can use for normal PCR?
I have some small secreted proteins which have the ability to move from plant to fungi. As they can move between plant and fungi, I assume these small secreted proteins have some domains responsible for their movement such as export and import domains. I am planning to generate a series of deletion constructs to identify domains that are responsible for protein movement. What might be the good experimental strategy to identify the domains? Is there any good system or experimental strategy that I can use for quick testing of my deletion constructs?
Thanks in advance
9 days ago I e-mailed a potential Ph.D. supervisor after reading about his research interests and publications. The following is the email that I have sent him
" Dear XXXXXX,
I am an XXXXXX student currently pursuing a B.Sc. in Biochemistry at McMaster University, with a current average of XXXXX, graduating in the upcoming spring. Modules covered in my degree include basic biology and chemistry, introductory immunology and virology courses, immunological principles in practice, as well as specific biochemistry courses on metabolism, stem cells, and protein structure and interactions.
I am strongly considering applying for a Ph.D. in Infection and Immunity at UCL. While browsing the Division of Infection and Immunity website, I noticed that your research of interest in T cell cancer Immunotherapy matches my desired area of specialization. In particular, I find the ideas of redirecting T cells against specific tumor malignancies, by using viral vectors to induce expression of TCRs and CARs to target specific antigens, co-stimulation of engineered T cells by cells in normal tissues, and CD3-enhanced T cells extremely fascinating and appealing as potential topics for a Ph.D.
I intend to secure funding either through a UCL or Research Council studentship and would consider self-funding my Ph.D. as an alternative option.
So far, my research experience includes an independent research project as well as a research thesis, which I am currently conducting, in a laboratory of Human Genetics and Mechanisms of Disease, XXXXXXXXXX.
I hope you do not mind my getting in touch, but I would like to enquire about whether you are currently accepting Ph.D. students who are looking to start a Ph.D. in fall 2020.
I am pleased to attach herewith my Academic CV, for your kind consideration, and would be delighted to discuss further details via Skype or by e-mail.
I appreciate your time and help and I look forward to hearing from you.
Is there something wrong with this email that may lead the Professor to avoid replying? I feel like I have provided enough information for him to decide whether or not he is interested in me as a member of his team. I also feel like I have shown interest in his research interests. Is it too soon to send a follow-up email inquiring about whether he has read my first email? I don't want to be inappropriate or, even worse, stress him, as I understand faculty members are busy.
Thank you in advance for your answers and help
I am a beginner in PopGen, and I am using smartPCA for my research. So far, I encountered several questions:
1. My genotype data is seperated by chromosome in each file. Currently I am testing my scripts with chr22 only. Do I need to pool them toghther in to one file to do smartPCA?
2. It seems that smartPCA will raise an error if the phenotype column in input file is empty (for instance, 0 for all individuals). However, I think phenotype data is not needed for PCA. Do I need the actual phenotype data to run the program?
I would like to know if results for copy number variants from pharmacogenetics testing labs typically are specific for allelic variants. For example,could the result reported as CYP2D6*1/*1N4 actually be CYP2D*1/*4N4?
What is the difference between methods of local ancestry inference that use Model background LD, such as SABER with methods of local ancestry inference that do not use Model background LD, such as RFMix?
Does using background linkage disequilibrium mean referring to the recombination in the model?
I appreciate your help.
I am a Ph.D biomedical engineering student.
My project is about genetic ancestry. I want to work on classification the genomes of an admixed population into different ancestries. Can this be a good topic for my project? Is the acceptance of the article in this field that related to human genetics is complicated and difficult?
I appreciate your help.
I'm working on NrCAM gene mutation. I'm searching to know about any known mutations recorded in NrCAM gene. But I'm not getting any databases or articles regarding that. Can anyone suggest me any mutation database or links to know about the mutations of NrCAM gene in humans.
I have very limited resources in my lab and very narrow budget. I used to use the red blood lysis solution, but I'm now trying to find a new protocol. Can anyone help?
The modern system of classification is based on evolutionary relationships among organisms – that is, on the organisms’ phylogeny. Classification systems based on phylogeny organize species or other groups in ways that reflect our understanding of how they evolved from their common ancestors.
I'm working on haplotypes case control association study, for data analysis , I employed two online analysis softwares ,
The first is (SNPstats) which gave me extremely large odd ratio values as showing in the attached snapshot .
the second is (http://analysis.bio-x.cn/myAnalysis.php) which gave me empty values (---) as showing in the attached snapshot . .
please , how can I explane this odd ratio values ,
thank for any help .
Hi, I identified a mutation that is very frequent and could represent a founder effect in Vietnam. I would like to know the time that has elapsed since the appearance of the common ancestor carriers in the population and the growth rate of the number of copies since this appearance.
CRISPR/Cas9 is a system found in bacteria and involved in immune defence. Bacteria use CRISPR/Cas9 to cut up the DNA of invading bacterial viruses that might otherwise kill them.
Today we’ve adapted this molecular machinery for an entirely different purpose – to change any chosen letter(s) in an organism’s DNA code.
Hi everyone, I am a fission yeast person and I am looking for a comprehensive list of codon occurrence on human transcriptome. I don't mean codon usage bias but something like
GlyGGG --> 12611 counts
GlyGGA --> 45350 counts
Any idea where I could find this?
Thanks in advance for your help! Best, Olivier
I know one can compute genetic distances between different population datasets, such as Fst, linearized Fst etc using Arlequin and Y-STR haplotype datasets. Some papers claim that they have used Arlequin to calculate Rsts, and I just can't see how? Any ideas? Many thanks in advance.
we know genetic is very complex plan in life. does this complex plan change with exercise?
does resistance training induce genetic changes? how?
does aerobic exercise induce genetic changes?
how can use from these changes for athletic purpose?
It should be noted that when requesting a DNA Investigation it is of VITAL importance that the DNA collection is carried out under completely controlled and scientific conditions and it is therefore important to contact us regarding the possible evidence BEFORE it is interfered with or contaminated. The accuracy and admissibility of the evidence is totally dependent on the procedures and controls used.
DNA Investigations will examine the DNA profile from two or more samples, and by identifying unique values in the DNA chain, these values can be compared to indicate whether or not there is a connection or relationship between them. Our service is carried out in complete confidence and trust.
Mitochondria are structures within cells that convert the energy from food into a form that cells can use. Although most DNA is packaged in chromosomes within the nucleus, mitochondria also have a small amount of their own DNA. This genetic material is known as mitochondrial DNA or mtDNA. In humans, mitochondrial DNA spans about 16,500 DNA building blocks (base pairs), representing a small fraction of the total DNA in cells.
Mitochondrial DNA contains 37 genes, all of which are essential for normal mitochondrial function. Thirteen of these genes provide instructions for making enzymes involved in oxidative phosphorylation. Oxidative phosphorylation is a process that uses oxygen and simple sugars to create adenosine triphosphate (ATP), the cell's main energy source. The remaining genes provide instructions for making molecules called transfer RNA (tRNA) and ribosomal RNA (rRNA), which are chemical cousins of DNA. These types of RNA help assemble protein building blocks (amino acids) into functioning proteins.
Several clones had been produced in the lab before Dolly, including frogs, mice, and cows, which had all been cloned from the DNA from embryos. Dolly was remarkable in being the first mammal to be cloned from an adult cell. This was a major scientific achievement as it demonstrated that the DNA from adult cells, despite having specialized as one particular type of cell, can be used to create an entire organism. Please, the question is that what are the steps for cloning of Dolly sheep?
It is well known that genes play an important role in controlling all biological activity in our life. Most of these are functional can either in gene expression or in the synthesis if protein......
Gene therapy is an insertion of functional gene in the location of dysfunctional gene or neighboring to it. we have just last week the first report of use of CRISPR technology to alter a human embryo — but these were not permitted to develop beyond a few days. So it demonstrated that, yes, you can use CRISPR to edit DNA of a human embryo — but you can’t call it a “successful gene therapy” yet because this was an “in the lab” technique, not one with a viable human patient.
The diffence between the two is the sequence information that is encoded. The tracrRNA or trans-activating crRNA is made of up of a longer stretch of bases that are constant and provide the “stem loop” structure bound by the CRISPR nuclease . When these RNA components hybridize they form a guide RNA which “programmably” targets CRISPR nucleases to DNA sequences depending on the complementarity of the crRNA and the presence of other DNA features (PAM sequence recognized by the nuclease).
At other of a naïve cells meaning, What is the probability that there will be activation of a naïve T cell bu an Antigen Presenting Cells (APCs)
A cell type is very scarce while isolated out and hard to expand in vitro. I ask here if there is any technique to expand one set of cell chromosome in vivo, or in vitro or ex vitro.
If you have twin brother who died at birth, and have been curious to know if you are identical or fraternal. Is there any specific test to determine that?
Dimensional shape of RNA forminf internal basepairs wherever its sequence allows...
Since most phenotypic characters and biochemical pathways in any living organism are based on its genetic background, is the updating of parasite's genome happens in response to the host genome evolution?
Please I would like to know the difference between exclusion mapping and homozygosity mapping and why we do exclusion mapping in some families and homozygosity mapping in other since they give somewhat similar results. What are the major differences?
I recently had a problem with protein purification in BL21, ran my sequence through a program linked to by a helpful Research Gate poster, and discovered that ~26% of my codons were reaching for tRNAs that represented <10% of the tRNAs for their respective amino acids.
I then ran my sequence through the optimizer linked below but have been checking the results manually as it is my first time and I'd like to understand better. Just a few of my codons have been switched for codons that actually represent fewer TRNAs for that amino acid than before. I am still at 0% below the above threshold overall but wanted to check in.
The ones I'm seeing most frequently are:
D: GAU (0.65) -> GAC (0.35)
F: UUU (0.57) -> UUC (0.43)
S: AGC (0.33) -> UCC (0.11)
Is there something besides codon usage that is taken into account during optimization processes? Additionally, if a bottleneck is ultimately avoided is there any tangible benefit in using a more common codon?
I am looking at genotypes caused by allele A and allele G. The minor allele is allele G with frequency 0.01. Consequently I did not get recessive homozygotes during genotyping of patient samples. So, is it necessary to test whether these genotypes are in HWE ?
We have an ABI 3730 and we would like to run it on. Of course together with the expanding need for providing BRCA test routinely in our country for a low enough price.
I can't find it online, can you please send to me the PDF protocol of the kit named "Bosphore PCR Product Purification Spin Kit" of Anatolia Gene Works.
There are various genes reported for as somatic variants (not germline) in breast cancer. So is it possible for clinician or doctor to say or confirm whether the individual is affected with breast cancer using his somatic mutation profile?
I want to identify exon region for different gene using digital filtering method. Is their any solution of this problem?
I understand CADD doesnt score nonsense, frameshift or splice. But even my missense variants are not scored.
I am doing gel-free RRBS protocol and sequencing on HiSeq2000.
I have a question about efficiency of bisulfite C to T conversion:
Authors and public tutorials affirm that one way to calculate bisulfite efficiency conversion is to observe all C residues in non-CpG positions in the sequence and calculate how many C are converted in T over the overall sequence.
But how many fragments should I read to have a overall idea of bisulfite efficiency conversion?
To estimate C to T efficiency conversion, I usually calculate how many times the CTP added in “end repair” step is converted in T: I expect, if I had a conversion efficiency of 100%, to see in each fragment I read a T nucleotide instead C.
How is your experience about this topic?
For clinical significance, what are the parameters should I consider for sequencing a sample. For example terms like High read depth
I am looking for the sequences of p53 pseudo-genes in different mouse species. It is on chromosome 14 (almost certain!) while the true p53 gene is on chromosome 11. Can I specify chromosome number in blast search, so that I only search against chromosome 14?
I am sorry if the question seems too simplistic. I am a junior faculty member transitioning to molecular biology from my earlier interest in oxidative stress and inflammation in disease.
I want to study whole genomes,instead of specific genes, of diseased cell, for epigenetic changes. My lab doesn't have a sequencer nor do I have funds or manpower to do a whole genome sequencing. I plan to use DNA electrophoresis along with immunoblotting using antibodies against methylated and hyroxymethylated cytosine to look for regions that are showing increased or decreased methylation in certain diseases. But before I even start to I need to know if it is possible do electrophoresis of the entire human DNA after breaking it into smaller pieces using an endonuclease. And is their any endonuclease that targets highly conserved regions of human DNA that would lead to a similar electrophoresis pattern emerging when DNA from different subjects is treated using it?
Hi. We have some trio pedigrees and performed whole exome sequencing. We wanted to confirm the relationship between the parents and the child. Is there any recommendations about programs for haplotype phasing and paternity test using WES data. Thanks!
Hello... Is anyone using plink for SNP analysis... I need some suggestions in this regard.. Thank you
FBAT software provides several different models to run family-based association test, such as dominant, recessive and additive. However, when I used PLINK software, I just can select --tdt, --dfam, or --qfam-total to do family-based association test. I don't know which model PLINK applied. I looked at the document and instruction, but I can't find answer. Does anyone know?
I am looking for an open bioinformatic program or script with the option of quick analyzing the presence or absence of nonsynonymous SNPs in the NGS results of amplicons of known proteins in a particular human individuals. The program of course may include mapping to the reference genomes but in principle it should detect known SNPs by analyzing the nucleotide sequence and finding a substitution in a codon causing a change in a known SNP position (triggering mutation to another amino acid). Mainly known substitutions are important, however detection of novel would be optional with mapping. I possibly would appreciate pointing to a few programs to fix them with a script. And it's not about dbSNP on NCBI or any other.