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Alleles notation in SNPPedia criteria

Alleles notation in SNPPedia criteria


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I can understand the allele notation when is in the form rs8176719(T;T) or rs8176719(G) but recently i found this ones rs8176719(T;-) or rs8176719(-;T).

So im confused, rs8176719(T;-) is the same as rs8176719(T)? or is the location is important ?

Thanks .


The '-' means that that allele has a single base deletion.


Alleles notation in SNPPedia criteria - Biology

Define genotype , phenotype , dominant allele , recessive allele , codominant alleles , locus , homozygous , heterozygous , carrier and test cross .

Genotype: the alleles of an organism.

Phenotype: the characteristics of an organism.

Dominant allele: an allele that has the same effect on the phenotype whether it is present in the homozygous or heterozygous state.

Recessive allele: an allele that only has an effect on the phenotype when present in the homozygous state.

Codominant alleles: pairs of alleles that both affect the phenotype when present in a heterozygote. (The terms incomplete and partial dominance are no longer used.)

Locus: the particular position on homologous chromosomes of a gene.

Homozygous: having two identical alleles of a gene.

Heterozygous: having two different alleles of a gene.

Carrier: an individual that has one copy of a recessive allele that causes a genetic disease in individuals that are homozygous for this allele.

Test cross: testing a suspected heterozygote by crossing it with a known homozygous recessive. (The term backcross is no longer used.)

Determine the genotypes and phenotypes of the offspring of a monohybrid cross using a Punnett grid.

The grid should be labelled to include parental genotypes, gametes, and both offspring genotype and phenotype .

Aim 7: Genetics simulation software is available.

State that some genes have more than two alleles (multiple alleles).

Describe ABO blood groups as an example of codominance and multiple alleles.

Explain how the sex chromosomes control gender by referring to the inheritance of X and Y chromosomes in humans.

State that some genes are present on the X chromosome and absent from the shorter Y chromosome in humans.

Describe the inheritance of colour blindness and hemophilia as examples of sex linkage.

Both colour blindness and hemophilia are produced by a recessive sex-linked allele on the X chromosome. X b and X h is the notation for the alleles concerned. The corresponding dominant alleles are X B and X H .

State that a human female can be homozygous or heterozygous with respect to sex-linked genes.

Explain that female carriers are heterozygous for X-linked recessive alleles.

Predict the genotypic and phenotypic ratios of offspring of monohybrid crosses involving any of the above patterns of inheritance.

Aim 8: Statisticians are convinced that Mendel’s results are too close to exact ratios to be genuine. We shall never know how this came about, but it offers an opportunity to discuss the need for scientists to be truthful about their results, whether it is right to discard results that do not fit a theory as Louis Pasteur is known to have done, and the danger of publishing results only when they show statistically significant differences.

TOK: Reasons for Mendel’s theories not being accepted by the scientific community for a long time could be considered. Other cases of paradigm shifts taking a long time to be accepted could be considered. Ways in which individual scientists are most likely to be able to convince the scientific community could be considered, and also the need always to consider the evidence rather than the views of individual scientists, however distinguished.

Deduce the genotypes and phenotypes of individuals in pedigree charts.

For dominant and recessive alleles, upper-case and lower-case letters, respectively, should be used. Letters representing alleles should be chosen with care to avoid confusion between upper and lower case.

For codominance, the main letter should relate to the gene and the suffix to the allele, both upper case. For example, red and white codominant flower colours should be represented as C R and C w , respectively. For sickle-cell anemia, Hb A is normal and Hb s is sickle cell.

Aim 8: There are many social issues in families in which there is a genetic disease, including decisions for carriers about whether to have children, personal feelings for those who have inherited or passed on alleles for the disease, and potential problems in finding partners, employment and health or life insurance. There are ethical questions about whether personal details about genes should be disclosed to insurance companies or employers. Decisions may have to be made about whether or not to have screening. These are particularly acute in the case of Huntington disease.


Alleles notation in SNPPedia criteria - Biology

2. Describe the consequences of a base substitution mutation with regards to sickle cell anemia. 7 marks

  • the sequence of nucleotide bases in DNA codes for the sequence of amino acids in proteins
  • DNA is transcribed into mRNA, which is translated into amino acids of protein
  • normal (ß chain) hemoglobin gene / DNA produces normal (ß chain) hemoglobin protein / amino acids
  • substitution= the replacement of one (or more) nucleotide base with another
  • caused by a copying mistake during DNA replication
  • as a result of a mutagen / X-rays / chemical / UV radiation / other mutagen
  • mutation in normal (ß chain) hemoglobin gene alters the sequence of nucleotide bases
  • normal nucleotide sequence = CTC altered to CAC
  • resulting in altered mRNA (GAG to GUG) during transcription
  • resulting in altered sequence of amino acids in (ß chain) hemoglobin protein (glutamic acid to valine) during translation
  • causing red blood cells to change shape / sickle under low oxygen conditions
  • causing sickle cells anemia when two copies of the mutated gene are inherited
  • producing a sickle cell carrier when one copy of the mutated gene is inherited
  • sickle cells anemia reduces oxygen flow to organs, leading to their deterioration

3. Explain how an error in meiosis can lead to Down syndrome. 8 marks

Accept the points below in an appropriately annotated diagram.

  • non-disjunction
  • chromosomes/chromatids do not separate / go to same pole
  • non-separation of (homologous) chromosomes during anaphase I
  • due to incorrect spindle attachment
  • non-separation of chromatids during anaphase II
  • due to centromeres not dividing
  • occurs during gamete/sperm/egg formation
  • less common in sperm than egg formation / function of parents' age
  • Down syndrome due to extra chromosome 21
  • sperm/egg/gamete receives two chromosomes of same type
  • zygote/offspring with three chromosomes of same type / trisomy / total 47 chromosomes

4. Karyograms involve arranging the chromosomes of an individual into pairs. Describe one application of this process, including the way in which the chromosomes are obtained. 5 marks

  • find gender / test for Down's syndrome / other chromosome abnormality
  • identify sex chromosomes / numbers of chromosome 21 / other chromosomes counted
  • XX = female and XY = male / third chromosome 21 indicates Down's syndrome / other chromosome abnormality (e.g. Klinefelter's syndrome)
  • fetal cells obtained from amniotic fluid / amniocentesis / other named source
  • white blood cells obtained
  • cells encouraged to divide
  • cells accumulated / blocked in metaphase
  • prepare slide / chromosomes examined

5. Compare the processes of mitosis and meiosis. 6 marks

answers must be pair-wise comparisons to receive any marks.

  • Mitosis: one cell division & Meiosis: two divisions / reduction division
  • Mitosis: chromosome number does not change & Meiosis: converts diploid to haploid cells
  • Mitosis: products genetically identical & Meiosis: products genetically diverse
  • Mitosis: separation of sister chromatids in anaphase & Meiosis: separation of homologous chromosomes in anaphase I and sister chromatids in anaphase II
  • Mitosis: no crossing over & Meiosis: crossing over in prophase I
  • Mitosis: no formation of tetrads / no synapsis & Meiosis: formation of tetrads / synapsis
  • Mitosis: produce cells for growth/repair/asexual reproduction & Meiosis: produce sexual cells / gametes for sexual reproduction
  • Mitosis: two cells produced & Meiosis: four cells produced
  • Mitosis: daughter cells with both copies of chromosomes/random assortment does not occur & Meiosis: random assortment of maternal/ paternal chromosomes
  • Mitosis: replication of DNA in interphase & Meiosis: replication of DNA in interphase I
  • Mitosis: four phases: prophase, metaphase, anaphase, telophase & Meiosis: same four phases twice

6. Outline one example of inheritance involving multiple alleles. 5 marks

  • multiple alleles means a gene has three or more alleles / more than two alleles
  • ABO blood groups / other named example of multiple alleles
  • ABO gene has three alleles / equivalent for other example
  • IA IB and i shown (at some point in the answer) / equivalent for other example
  • any two of these alleles are present in an individual
  • homozygous and heterozygous genotye with phenotypes (shown somewhere)
  • all six genotypes with phenotypes given (shown somewhere)
  • example / diagram of a cross involving all three alleles

7. Describe the inheritance of ABO blood groups including an example of the possible outcomes of a homozygous blood group A mother having a child with a blood group O father. 5 marks

  • example of co-dominance
  • multiple alleles / 3 alleles
  • (phenotype) O has (genotype) ii
  • B can be IB IB or IB i
  • A can be IA IA or IA i
  • AB is IA IB
  • (P are) i i x IA IA
  • (gametes) i and IA
  • (F1 genotype) IA i
  • (F1 phenotype) blood group A

8. Outline sex linkage. 5 marks

  • gene carried on sex chromosome / X chromosome / Y chromosome
  • inheritance different in males than in females
  • males have only one X chromosome therefore, only one copy of the gene
  • mutation on Y chromosome can only be inherited by males
  • women can be carriers if only one X chromosome affected
  • example of sex linked characteristics (e.g. hemophilia / color blindness)
  • example of cross involving linkage

9. Explain, using a named example, why many sex-linked diseases occur more frequently in men than women. 9 marks

  • named example of sex-linked disease
  • caused by recessive allele
  • on the X chromosome
  • example of pair of alleles (e.g. X H and X h) (reject if alleles do not correspond)
  • females are XX and males are XY
  • females have two alleles of the gene and males have only one
  • allele causing the disease is rare / uncommon
  • probability of femles inheriting rare allele twice as low
  • calculation of squaring the gene frequency
  • female would have to inherit the allele from her father
  • who would have suffered from the disease
  • so females can carry the gene but still be normal
  • but males (with the gene) will have the disease

10. Outline the formation of chiasmata during crossing over. 5 marks


Help me interpret some SNPs pretty please

Since I don't have much of a life, I went through my results for SNPs on the PAH gene from 23andme, and compared their reported alleles with those listed on this page in SNPedia.

I have three areas of concern:

SNPMy GenotypeSNPedia link
rs62508727TGA/TGAhttps://www.snpedia.com/index.php/Rs62508727
rs63749677-/-https://www.snpedia.com/index.php/Rs63749677
rs62642941-/-https://www.snpedia.com/index.php/Rs62642941

For this first SNP, TCA/TCA is reported as common in clinvar. My genotype reported by 23andme, TGA/TGA isn't even in the list. Would a misread be responsible for this?

For the second, the pathogenic mutation is reported as genotype -/16. My genotype is reported as -/-. How should I interpret this?

The third, I figure, is pretty straightforward. Correct me if I'm wrong.

However, for PKU or variants, I would need to have two mutations of PAH. Since I'm not sure how to interpret the first two of these SNPs, I can't really come to any conclusion.

Should I bring up these results with a physician, or chalk up my results to 23andme messing up a few things?


The Chromosome Theory of Linkage:

E. Castle and T. H. Morgan reported ‘The Chromosome Theory of Linkage’.

It has the following important features:

  1. Genes that display linkage are situated in the one chromosome.
  2. Genes are placed in a linear fashion in the chromosome, i.e., linkage of genes is lineal.
  3. The space between the linked genes is inversely proportional to the capacity of linkage. The genes which are closely seated show strong linkage, whereas those, which are enlargely separated, have more scope to get separated by crossing over (weak linkage).
  4. Linked genes remain in their main combination during the course of inheritance.
  5. The linked genes indicate two types of orders on the chromosome strands. If the dominant alleles of 2 or more couples of linked genes are present on one chromosome and their recessive alleles of all of them on the other homologue (AB/ab), this arrangement is known as cis arrangement. However, if the dominant allele of one pair and recessive allele of the second pair are present on one chromosome and recessive and dominant alleles on the other chromosome of a homologous pair (Ab/aB), this arrangement is called a trans arrangement.

Alleles notation in SNPPedia criteria - Biology

2. Describe the consequences of a base substitution mutation with regards to sickle cell anemia. 7 marks

  • the sequence of nucleotide bases in DNA codes for the sequence of amino acids in proteins
  • DNA is transcribed into mRNA, which is translated into amino acids of protein
  • normal (ß chain) hemoglobin gene / DNA produces normal (ß chain) hemoglobin protein / amino acids
  • substitution= the replacement of one (or more) nucleotide base with another
  • caused by a copying mistake during DNA replication
  • as a result of a mutagen / X-rays / chemical / UV radiation / other mutagen
  • mutation in normal (ß chain) hemoglobin gene alters the sequence of nucleotide bases
  • normal nucleotide sequence = CTC altered to CAC
  • resulting in altered mRNA (GAG to GUG) during transcription
  • resulting in altered sequence of amino acids in (ß chain) hemoglobin protein (glutamic acid to valine) during translation
  • causing red blood cells to change shape / sickle under low oxygen conditions
  • causing sickle cells anemia when two copies of the mutated gene are inherited
  • producing a sickle cell carrier when one copy of the mutated gene is inherited
  • sickle cells anemia reduces oxygen flow to organs, leading to their deterioration

3. Outline the formation of chiasmata during crossing over. 5 marks

Accept the points below in an appropriately annotated diagram.

  • crossing over/chiasmata formed during prophase I of meiosis
  • pairing of homologous chromosomes/synapsis
  • chromatids break (at same point) (do not accept chromatids overlap)
  • non-sister chromatids join up/swap/exchange alleles/parts
  • X-shaped structure formed / chiasmata are X-shaped structures
  • chiasma formed at position where crossing over occurred
  • chiasmata become visible when homologous chromosomes unpair
  • chiasma holds homologous chromosomes together (until anaphase) 5 max

4. Explain how an error in meiosis can lead to Down syndrome. 8 marks

Accept the points below in an appropriately annotated diagram.

  • non-disjunction
  • chromosomes/chromatids do not separate / go to same pole
  • non-separation of (homologous) chromosomes during anaphase I
  • due to incorrect spindle attachment
  • non-separation of chromatids during anaphase II
  • due to centromeres not dividing
  • occurs during gamete/sperm/egg formation
  • less common in sperm than egg formation / function of parents' age
  • Down syndrome due to extra chromosome 21
  • sperm/egg/gamete receives two chromosomes of same type
  • zygote/offspring with three chromosomes of same type / trisomy / total 47 chromosomes

5. Karyotyping involves arranging the chromosomes of an individual into pairs. Describe one application of this process, including the way in which the chromosomes are obtained. 5 marks

application of karyotyping

  • find gender / test for Down's syndrome / other chromosome abnormality
  • identify sex chromosomes / numbers of chromosome 21 / other chromosomes counted
  • XX = female and XY = male / third chromosome 21 indicates Down's syndrome / other chromosome abnormality (e.g. Klinefelter's syndrome)
  • fetal cells obtained from amniotic fluid / amniocentesis / other named source
  • white blood cells obtained
  • cells encouraged to divide
  • cells accumulated / blocked in metaphase
  • prepare slide / chromosomes examined

6. Compare the processes of mitosis and meiosis. 6 marks

answers must be pair-wise comparisons to receive any marks.

  • Mitosis: one cell division & Meiosis: two divisions / reduction division
  • Mitosis: chromosome number does not change & Meiosis: converts diploid to haploid cells
  • Mitosis: products genetically identical & Meiosis: products genetically diverse
  • Mitosis: separation of sister chromatids in anaphase & Meiosis: separation of homologous chromosomes in anaphase I and sister chromatids in anaphase II
  • Mitosis: no crossing over & Meiosis: crossing over in prophase I
  • Mitosis: no formation of tetrads / no synapsis & Meiosis: formation of tetrads / synapsis
  • Mitosis: produce cells for growth/repair/asexual reproduction & Meiosis: produce sexual cells / gametes for sexual reproduction
  • Mitosis: two cells produced & Meiosis: four cells produced
  • Mitosis: daughter cells with both copies of chromosomes/random assortment does not occur & Meiosis: random assortment of maternal/ paternal chromosomes
  • Mitosis: replication of DNA in interphase & Meiosis: replication of DNA in interphase I
  • Mitosis: four phases: prophase, metaphase, anaphase, telophase & Meiosis: same four phases twice

7. Outline one example of inheritance involving multiple alleles. 5 marks

  • multiple alleles means a gene has three or more alleles / more than two alleles
  • ABO blood groups / other named example of multiple alleles
  • ABO gene has three alleles / equivalent for other example
  • IA IB and i shown (at some point in the answer) / equivalent for other example
  • any two of these alleles are present in an individual
  • homozygous and heterozygous genotye with phenotypes (shown somewhere)
  • all six genotypes with phenotypes given (shown somewhere)
  • example / diagram of a cross involving all three alleles

8. Describe the inheritance of ABO blood groups including an example of the possible outcomes of a homozygous blood group A mother having a child with a blood group O father. 5 marks

  • example of co-dominance
  • multiple alleles / 3 alleles
  • (phenotype) O has (genotype) ii
  • B can be IB IB or IB i
  • A can be IA IA or IA i
  • AB is IA IB
  • (P are) i i x IA IA
  • (gametes) i and IA
  • (F1 genotype) IA i
  • (F1 phenotype) blood group A

9. Outline sex linkage. 5 marks

  • gene carried on sex chromosome / X chromosome / Y chromosome
  • inheritance different in males than in females
  • males have only one X chromosome therefore, only one copy of the gene
  • mutation on Y chromosome can only be inherited by males
  • women can be carriers if only one X chromosome affected
  • example of sex linked characteristics (e.g. hemophilia / color blindness)
  • example of cross involving linkage

10. Explain, using a named example, why many sex-linked diseases occur more frequently in men than women. 9 marks


Lecture notes

1. Define genetic terms:

  • genotype: the alleles possessed by an organism
  • phenotype: the characteristics of an organism
  • dominant allele: an allele that has the same effect on the phenotype whether it is present in the homozygous or heterozygous state
  • recessive allele: an allele which only has an effect on the phenotype when present in the homozygous state
  • codominant alleles: pairs of alleles that both affect the phenotype when present in a heterozygote
  • locus: the particular position on homologous chromosomes of a gene
  • homozygous: having the two identical alleles of a gene
  • heterozygous: having two different alleles of a gene
  • carrier: an individual that has a recessive allele of a gene that does not have an effect on their phenotype
  • test cross: testing a suspected heterozygote by crossing with a known homozygous recessive

2. Determine the genotypes and phenotypes of the offspring of a monohybrid cross using a Punnett Grid:

3. State that some genes have more than two alleles (multiple alleles).

4. Describe ABO blood groups as an example of codominance and multiple alleles

5. Explain how the sex chromosomes control gender by referring to the inheritance of X and Y chromosomes of humans.

6. State: some genes are present on the X chromosome and absent from the shorter Y chromosome in humans

7. Define: sex linkage = genes carried on the sex chromosomes, most often on the X chromosome

8. Describe the inheritance of color blindness and hemophilia as examples of sex linkage.

9. State that a human female can be homozygous or heterozygous with respect to sex-linked genes.

10. Explain that female carriers are heterozygous for X-linked alleles.

  • heterozygous female carriers do not show the disease
  • but can pass it on to half of their male offspring

11. Predict the genotypic and phenotypic ratios of offspring of monohybrid crosses involved any of the above patterns of inheritance.

12. Deduce the genotypes or phenotypes of individuals in pedigree charts.


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We are involved in the genetically based numerical terminology for red cell surface antigens. By definition, these antigens must be defined serologically by the use of specific antibodies. All antigens receive a unique ISBT number and must have been shown to be inherited characters. We advise, maintain and monitor the terminology for blood group genes and genetic classification for blood group antigens. We offer members the opportunity to participate in the development/maintenance of nomenclature. We discuss all issues related to molecular typing as well as the analysis of blood group genes.

Our Chairpersons are Catherine Hyland and Christoph Gassner.


Author information

Glenn Hickey, David Heller and Jean Monlong contributed equally to this work.

Affiliations

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA

Glenn Hickey, David Heller, Jean Monlong, Jonas A. Sibbesen, Jouni Sirén, Jordan Eizenga, Erik Garrison, Adam M. Novak & Benedict Paten

Max Planck Institute for Molecular Genetics, Berlin, Germany

Department of Genetics, University of Cambridge, Cambridge, UK

Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA

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Contributions

EG, AN, GH, JS, JE, and ED implemented the read mapping and variant calling in the vg toolkit. GH, DH, JM, JAS, and EG performed analysis on the different datasets. GH, DH, JM, and BP designed the study. GH, DH, and JM drafted the manuscript. All authors read, reviewed, and approved the final manuscript.

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