Category Archives: Genetics

Ein echter Coup

23.01.2023 admin

Er hat seit September einen Twitter Account.

Anfang Januar hat er mit einer Bloggerin geredet (“Jesus ist die Inspiration für meine Arbeit, er opferte sich selbst um die Menschheit zu retten”).

Matthias Sander hat ihn nun aufgetrieben und für die NZZ interviewt: Dr. He Jiankui (“JK”) der Genetiker der Crispr Cas Twins, von dem Nobelpreisträger Baltimore sagt

Everyone deserves a second chance, but He Jiankui’s mistake was so colossal that I would never agree to funding his new experiments in biomedicine.

Was mich interessiert ist weniger sein Score im Golf oder daß er immer noch dasselbe Aktentäschchen wie auf der Bühne des Hongkong Summits trägt, sondern wie es den Kinder geht.

Continue reading Ein echter Coup →

Genetics

Genetic heritage and language does not always match

16.12.2022 admin

This is the interesting outcome of a new PNAS paper (pdf, R) that finds

According to the farming/language dispersal hypothesis, migrations fueled by the shift toward agriculture and animal husbandry in the Holocene have given rise to some of the largest language families identifiable today.

Most researchers thought that genes and language would match while the new paper shows

At the level of individual populations, we estimate more matches (matching enclaves or aligned populations) than mis- matches, but single-population mismatches are present in each continent and within each language family.

The database can be found at https://gelato.clld.org/

Allergy, Genetics, Vitamins

Allergy GWAS hits in VDR binding sites

30.11.2022 admin

It seems that I missed an interesting 2017 paper that looked for disease-associated SNPs in canonical DR3 motifs. Only 7 out of 211 traits showed significant hits, one of these was self-reported allergy. When annotating these SNPs, there are only two genes: LINC00299 and TLR1

hg38 position
rs10174949 2:8302018 LINC00299
rs10178845 2:8303773 LINC00299
rs5743566 4:38804221 TLR1
rs2101521 4:38809830 TLR1
rs5743565 4:38804262 TLR1
rs45588337 4:38805607 TLR1
rs55830619 4:38805643 TLR1

So are TLR1 & LINC00299 variant carriers more susceptible to vitamin D induced allergy?

LINC00299 (Long Intergenic Non-Protein Coding RNA 299) is a RNA Gene of largely unknown function, associated so far with allergy only on a genetic level in Framingham, href=”https://pubmed.ncbi.nlm.nih.gov/23817569/”>23andme and other studies. We don’t know so much here, the function of the long non coding RNAs

depends on subcellular localization. Depending on their niche, they specifically interact with DNA, RNA, and proteins and modify chromatin function, regulate transcription at various stages, forms nuclear condensation bodies and nucleolar organization. lncRNAs may also change the stability and translation of cytoplasmic mRNAs and hamper signaling pathways. Thus, lncRNAs affect the physio-pathological states and lead to the development of various disorders, immune responses, and cancer.

The TLR1 genetic association is found by many genetic studies, while the clinical association is probably more by an infectious origin. TLR1 is a pattern recognition receptor with a specificity for gram-positive bacteria and also included in my forthcoming exome paper as a protective factor for asthma/allergy. And we are also close to my earlier review of vitamin D, the microbiome and allergy…

Does any co-infection response during first vitamin D exposure influence allergic sensitisation? There are indeed some hints of an short-lived effect of lung group 2 innate lymphoid cells (ILC2s)

Laboratory mice cohoused for 2 weeks had impaired ILC2 responses and reduced lung eosinophilia to intranasal allergens, whereas these responses were restored in mice cohoused for ≥2 months. … These findings suggest that ILC2s respond dynamically to environmental cues and that microbial exposures do not control long-term desensitization of innate type 2 responses to allergens.

Allergy, Genetics

JACI – retractions overdue

1.08.2022 admin

JACI is the journal with the poorest experience that I ever encountered as an author and as a reviewer. The editors never adequately responded to numerous errors in an earlier paper where I sent a long letter describing all details.

And it is a nightmare – even now with more than 100 corrigenda in this journal – as the editorial office even modified correctly submitted images. Yes, the JACI editor published also falsified data.

Only recently I also found another strange retraction note

The Publisher regrets that this article is an accidental duplication of an article that has already been published in J Allergy Clin Immunol

while the link of this retraction note goes to https://pubmed.ncbi.nlm.nih.gov/24892183 which is, however, a different paper.

It seem that the journal already lost the overview…

Allergy, Genetics, Password

Allergy protection at farms, an epidemiological fallacy

5.06.2022 admin

This content has restricted access, please type the password below and get access.

Genetics

Longevity update

26.04.2022 admin

grg.org/WSRL/TableE.aspx has an update of our 2010 paper about longevity

and well, there is also an update on German centenarians

https://www.destatis.de/DE/Presse/Pressemitteilungen/Zahl-der-Woche/2022/PD22_28_p002.html

Allergy, Genetics

The Lancet and scientific integrity

21.04.2022 admin

We have learned in the past that the Lancet published editorials that clearly separated the journal from the publisher Elsevier

Reed Elsevier’s response is that the sale of military equipment is legal, government supported, and tightly regulated. However, The Lancet‘s collaborations in child survival and health-systems strengthening, for example, risk being tainted by Reed Elsevier’s promotion of the “selling process” of arms.

Of course you can’t sell weapons and distance yourself from selling weapons at the same time…

Pages: 1 2 3 4 5

Genetics

Hapmap

21.03.2022 admin

I find it increasingly difficult to get the haplotype structure of a given gene. While the are patches to the human genome at UCSC, this isn’t the same like good old hapmap.org by the HapMap consortium that has been retired back in 2016.

A recent computer security audit has revealed security flaws in the legacy HapMap site that require NCBI to take it down immediately. We regret the inconvenience, but we are required to do this. That said, NCBI was planning to decommission this site in the near future anyway (although not quite so suddenly), as the 1,000 genomes (1KG) project has established itself as a research standard for population genetics and genomics. NCBI has observed a decline in usage of the HapMap dataset and website with its available resources over the past five years and it has come to the end of its useful life.

It seems that also its successor, the 1000 genomes, will be retired during the next month. Unfortunately, the phasing server in Michigan does not allow any logon for whatever reason, UK biobank is too expensive so haplotypes basically vanished in the nirvana.

Genetics

Medizinische Blickdiagnose

15.03.2022 admin

Es gab schon immer Lehrbücher der Blickdiagnose. Dazu gibt es auch schon länger AI basierte Programme, die automatisiert Röntgen-, CT- oder PET Bilder erkennen und Diagnosen zuordnen können. Aber ein neuer Beitrag in nature genetics zeigt eine neue faszinierende Methode der schwierigen Diagnose genetischer Syndrome per Bildanalyse. Nach längerer Vorbereitung wurden hier 17.560 Patienten mit 1.115 Krankheiten in einem Datensatz erfasst. Die Zuordnung sollte damit auch für weniger erfahrene Experten leichter möglich sein. Das alles erinnert mich an ein mehrtägiges Frauenradrennen, das ich einmal fotografiert habe. Mit den täglichen Bildern auf der Siegertribüne liess sich auch ganz ohne KI die Zyklusschwankungen erkennen, allerdings nicht bei allen Teilnehmerinnen (V.a. funktionelle Amenorrhoe)

Allergy, Genetics

What did Sequana really find at Tristan da Cunha?

16.02.2022 admin

The Tristan da Cunha asthma study was leading to patent US6087485A. The patent describes

highly significant linkage in the genome scan (p=0.0001 for history of asthma and p=0.0009 for methacholine challenge) … at D11S907, a marker on the short arm of chromosome 11.

D11S907 or AFM109YA1 is a microsatellite marker located at 11p13 in a gene known as EHF (ETS homologous factor). There should be 2 genes in close proximity of the marker: ASTH1I and ASTH1J.

ASTH1I and ASTH1J were detected by exon trapping. ASTH1I exons detected a 2.8 kb mRNA expressed at high levels in trachea and prostate, and at lower levels in lung and kidney …
ASTH1J exons detected a 6.0 kb mRNA expressed at high levels in the trachea, prostate and pancreas and at lower levels in colon, small intestine, lung and stomach.

The sequences of table 2 in the patent are sufficient now to locate ASTH1I and ASTH1J. Continue reading What did Sequana really find at Tristan da Cunha? →

Allergy, Genetics

25 years Transatlantic Airway Conference 1997 on asthma genetics in Key Biscayne

Gallery 12.02.2022 admin

The conference series started in 1986 while the 12th conference was organized by Jeff Drazen with local support of Adam Wanner.

Sponsored by Boehringer Ingelheim, the participant list is the WHO is WHO in pulmonary genetics at that time: Bleecker, Meyers, Woolcock, Weiss, Burrows, Postma, Kauffmann, Dizier, LeSouef, Blumenthal, Banks-Schlegel, Slutsky, Zamel, Ober, Bousquet, Vercelli, Barnes, Adcock, Dahlen, Pauwels, Lewitt, Aron, Martinez, Cookson, Moffatt, Rosenwasser, Liggett, Rich, Papadopoulos, Levitt, Holgate, Elston, Morton and Marsh. Many of them do not live any more [1,2,3,4,5], some have made big careers [1,2], others have been fallen somewhat into disgrace [1,2,3] and many already retired. Continue reading 25 years Transatlantic Airway Conference 1997 on asthma genetics in Key Biscayne →

Genetics

Lander landed

8.02.2022 admin

He basically killed one of my best papers by the Kruglyak-Lander rule of what is being “significant”. He started the stupid CRISPR origin discussion. But now he steps down

President Biden’s top science adviser Eric Lander resigned on Monday after an investigation revealed he violated the White House‘s workplace policy by mistreating staff members

details at dailymail.co.uk

Lander ‘retaliated against staff for speaking out and asking questions by calling them names, disparaging them, embarrassing them in front of their peers, laughing at them, shunning them, taking away their duties, and replacing them or driving them out of the agency. Numerous women have been left in tears, traumatized, and feeling vulnerable and isolated,’ Wallace told the outlet.

Statnews has a good commentary about “The fall of Eric Lander and the end of science’s “big ego’ era”

It’s not quite “big science,” which isn’t going anywhere. Call it “big ego.” In science, “big ego” isn’t exactly a new phenomenon. But in recent decades it grew with the emergence of researchers who could both handle the kind of gloves-off debate that can mark academic discourse and marshal vast resources to make certain types of scientific discoveries, like mapping genomes.

Genetics, Philosophy

What is needed is a confrontational approach

1.02.2022 admin

Google showed me today a long forgotten abstract. Although I am not an expert in schizophrenia we collaborated two decades ago on this particular chromosomal region.

What is even more remarkable is the challenging keynote of the Xth World Congress of Psychiatric Genetics in The Palais des Congre ́s Brussels, Belgium October 9 –13, 2002 by Irving Gottesman [+2016], the father of epigenetics in psychiatry. He wrote there

We cannot escape the history of our field and are constantly guided today by the accumulation of facts with either positive or negative valences from our past. But when did the clock start—with the domestication of animals, with Galton’s musings and amoral passion for data collection about individual differences in behavior, or with the initially objective scientizing of Mendelism applied to schizophrenia but ending with a Nazi-tainted albatross around the neck of psychiatric genetics. In regard to the long quest for the distal and genetic (partial) causes of mental diseases, the conclusion that both genetic and environmental factors, none yet known in detail, provide the distal causes of mental disorders—that statement is too general to be of use to making further progress. What is needed is a confrontational approach based on evidence collected from competing ‘schools of thought’, and then reconciliation before some kind of omniscient and impartial Science Court.

I couldn’t agree more. What is needed is a confrontational approach based on evidence collected from competing ‘schools of thought’, and then reconciliation before some kind of omniscient and impartial Science Court.

Allergy, Genetics

Censored IL33 research

17.01.2022 admin

the AMGEN website …